ASSET TRANSFER AGREEMENT

Exhibit 10.12

EXECUTION COPY

ASSET TRANSFER AGREEMENT

This Asset Transfer Agreement (this “ Agreement ”) dated as of June 17, 2009, is entered into by and between Zygo Corporation, a Delaware corporation (“ Zygo ”), and Nanometrics Incorporated, a Delaware corporation (“ Nano ”).

RECITALS

A. Zygo has developed and is the owner of certain technology related to interferometers (the “ Automated Interferometers ”), including the “heads,” the control, monitoring and analysis software, and electronic control systems, as well as the automation of the systems that use these technologies.

B. Zygo seeks to establish a relationship with Nano, and Nano intends to establish a relationship with Zygo, pursuant to which Nano becomes the exclusive provider of the product referred to by Zygo as the “ Unifire ” and other Approved Systems (as defined below) in the Approved Markets (as defined below) that incorporate Heads (as defined below), subject to the terms and conditions hereof, and in that certain Supply Agreement, dated as of the Closing Date, by and between Zygo and Nano, attached hereto as Exhibit D (the “ Supply Agreement ”).

AGREEMENT

In consideration of the foregoing and the respective representations, warranties, covenants and agreements contained in this Agreement and the Supply Agreement, and other good and valuable consideration, the receipt and sufficiency of which each of the parties hereby acknowledges, and intending to be legally bound hereby, the parties agree as follows:

ARTICLE I

PURCHASE OF ASSETS AND ASSUMPTION OF LIABILITIES

1.1 Transfer of Assets . Upon and subject to the terms and conditions of this Agreement, Zygo shall transfer, convey, assign and deliver to Nano at the Closing, for the consideration specified in Section 1.3 below, (a) all right, title and interest in, to and under the Acquired Assets (which are listed on Schedule A-1 hereto), and (b) subject to Section 4.6 hereof, all its rights and obligations under the Assigned Contracts (which are listed on Schedule A-2 hereto).

1.2 Assumption of Liabilities . Upon and subject to the terms and conditions of this Agreement, Nano shall assume as of the Closing and become responsible for the Assumed Liabilities (which are listed on Schedule B hereto).

1.3 Consideration . The consideration for the transfer of assets is the execution of the Supply Agreement and this Agreement, and the related covenants of Nano hereunder and thereunder.

1.4 The Closing .

(a) The Closing shall take place at the offices of Fulbright & Jaworski L.L.P. in New York, New York, commencing at 1:00 p.m. local time on the Closing Date. All transactions at the Closing shall be deemed to take place simultaneously, and no transaction shall be deemed to have been completed and no documents or certificates shall be deemed to have been delivered until all other transactions are completed and all other documents and certificates are delivered.

(b) At the Closing:

(i) Zygo shall execute and deliver to Nano a bill of sale in the form attached hereto as Exhibit A (the “ Bill of Sale ”), and such other instruments of conveyance as Nano may reasonably request in order to (A) effect the sale, transfer, conveyance and assignment to Nano of valid ownership of the Acquired Assets, and (B) subject to Section 4.6 hereof, assign to Nano all its rights and obligations under the Assigned Contracts;

(ii) Zygo shall deliver to Nano, or otherwise put Nano in possession and control of, all of the Acquired Assets of a tangible nature;

(iii) Nano and Zygo shall execute and deliver to each other a cross-receipt evidencing the transactions referred to above;

(iv) Nano shall execute an instrument of assumption in substantially the form attached hereto as Exhibit B (the “ Assumption Agreement ”) to effect the assumption of the Assumed Liabilities;

(v) Nano and Zygo shall execute and deliver to each other the Supply Agreement; and

(vi) Nano and Zygo shall execute and deliver to each other the Sublease Agreement.

(c) As soon as practicable after the Closing, but in any event prior to the shipment by Zygo to Nano of the Purchased Inventory or the Demo Equipment, Nano shall execute and deliver to Zygo a security agreement granting Zygo a first perfected security interest in the Purchased Inventory and Demo Equipment (as later defined), and a corresponding UCC-1 financing statement, both in a form reasonably acceptable to Zygo, to ensure Zygo’s receipt of the Purchased Inventory Purchase Price and Demo Equipment Purchase Price or the return of such transferred assets.

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1.5 Sublease of Hillsboro Facility .

(a) At Closing, Nano and Zygo shall enter into a sublease agreement (the “ Sublease Agreement ”) pursuant to which Nano will sublease from Zygo, and Zygo will sublease to Nano, Zygo’s facility located at 2925 N.W. Aloclek Drive, Suite # 100 Hillsboro, Oregon (the “ Oregon Facility ”), consisting of 6,410 square feet of space, through December 31, 2012, for monthly rent in an amount equal to the current base rent and any other charges otherwise payable by Zygo under its existing lease of the Oregon Facility.

(b) As of the Closing, Nano and Zygo agree as follows

(i) Zygo hereby leases to Nano and Nano hereby leases from Zygo, for the monthly rent equal to the amortization of the fixed assets described in Section 2.15 of Exhibit C over the life of the Sublease Agreement based on an interest rate of zero percent, the Personal Property (as hereinafter defined) on the terms and conditions of this Section 1.5(b). The term “ Personal Property ” means certain improvements, furniture, phone system and fixed assets described in Section 2.7 of Exhibit C . This lease of Personal Property shall expire and terminate at such time the Sublease Agreement shall expire or earlier terminate. This lease of Personal Property and any conveyance of Personal Property are made AS-IS, WHERE-IS, without any warranty of merchantability of suitability for any particular purpose, all rights waived by Nano.

(ii) Nano shall maintain the Personal Property in its existing condition, ordinary wear and tear excepted, at its sole cost and expense. Nano shall bear the entire risk of loss or damage to the Personal Property during the term of this lease, and Nano shall insure the Personal Property at all times against risks of loss or damage by fire, theft and such other risks as may be covered by the insurance generally carried by Nano in respect of its personal property. All insurance proceeds shall be payable to Nano, and Nano shall pay to Zygo all insurance proceeds paid to Nano in respect of the Personal Property. Nano may not remove the Personal Property from the Oregon Facility without the consent of Zygo. Nano shall not grant any security interest in the Personal Property or in any other manner assign, pledge, hypothecate, mortgage, lease, sublease, encumber or otherwise transfer the Personal Property or its interest in the Personal Property.

(iii) Upon termination of this lease of Personal Property, Nano shall return the Personal Property to Zygo in the condition in which it was leased to Nano, ordinary wear and tear excepted.

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1.6 Payment for Inventory .

(a) Nano is purchasing the inventory described in Schedule A-1 (the “ Purchased Inventory ”) for $2,014,000, subject to adjustment after Closing pursuant to Section 1.6(c) hereof (the “ Purchased Inventory Purchase Price ”). Nano shall pay for the Purchased Inventory in the manner described in this Section. Within ten (10) days after the end of the month in which Nano receives payment on the sale by Nano of each Automated Interferometer System that includes Purchased Inventory, Nano shall pay to Zygo an amount equal to the price paid to Nano by Nano’s customer for such entire system (adding back the dollar amount of any set-offs or other types of credits, or reductions to the purchase price actually applied, for amounts Nano may otherwise owe to such customer) but reducing such by the cost of the Head included in the Automated Interferometer System (which will be paid for in accordance with the Supply Agreement), to be applied toward the Purchased Inventory Purchase Price, until the total Purchased Inventory Purchase Price has been paid in full, and thereafter to the Demo Equipment Purchase Price (as defined below) until such amount has been paid in full. For example, if Nano sells an Automated Interferometer System for $1,200,000 that includes any Purchased Inventory, and the outstanding balance of the Purchased Inventory Purchase Price exceeds $1,200,000 at the time of such sale, then Nano shall pay to Zygo the amount of $1,200,000 less the cost of the Head included in such System (which will be paid for in accordance with the Supply Agreement) within ten (10) days after the end of the month in which Nano receives payment from Nano’s customer, and such amount shall be applied toward the outstanding balance of the Purchased Inventory Purchase Price.

(b) Nano hereby agrees that, from and after the Closing Date until such time as the Purchased Inventory Purchase Price and the Demo Equipment Purchase Price have been paid in full (or, in the case of subsection (b)(v) below, until 30 days following the calendar quarter during which the last of such outstanding amounts shall have been paid in full):

(i) in the production of any Automated Interferometer System, Nano shall first utilize the Purchased Inventory prior to utilizing alternatively available inventory

(ii) Nano shall not use Purchased Inventory for any purpose other than the production of such systems or in connection with providing warranty service or other service with respect to Automated Interferometer Systems sold by Zygo or by Nano;

(iii) Nano shall sell the Automated Interferometer System for cash consideration (including a check or money order) and shall set pricing based on its standard practices for ordinary course arms-length third party transactions (“ Standard Prices ”);

(iv) Nano shall make diligent efforts, consistent with its historical practice, to collect payment for all sales of its Automated Interferometer Systems as to which all or any portion of such payment shall be paid to Zygo pursuant to the provisions of Sections 1.6 and/or 1.7 hereof; and

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(v) No later than 30 days following each calendar quarter, Nano will provide Zygo with a statement of its sales of Automated Interferometer Systems, certified by Nano’s Chief Financial Officer. Upon reasonable notice, and at Zygo’s cost and expense, Nano will permit Zygo and its representatives to audit Nano’s books and records as they pertain to sales of Automated Interferometer Systems; provided that if an audit reveals discrepancy of greater than the lesser of (x) $50,000 or (y) five (5) times aggregate dollar sales, then the cost and expense of such audit shall be borne by Nano.

(c) No later than fifteen (15) business days after the Closing Date, Zygo shall perform a physical inventory on the Purchased Inventory in accordance with generally accepted accounting principles applied consistently with Zygo’s past practices. Nano, or their respective representatives, shall observe the taking of the inventory at its sole cost and expense. Disputes between Zygo and Nano with respect to the merchandise inventory shall be resolved by Zygo and Nano at the time the physical inventory is being taken. The results of the inventory shall conclusively be deemed to be the Purchased Inventory for purposes of this Agreement. As part of this inventory, Zygo shall determine the book value of the Purchased Inventory as of the Closing Date, in accordance with generally accepted accounting principles applied consistently with Zygo’s past practices. The determination of the book value of the Purchased Inventory as of the Closing Date pursuant to this Section 1.6(c), shall, for all purposes of this Agreement, be the Purchased Inventory Purchase Price. All work sheets used in determining the foregoing shall be signed by Zygo and Nano or their respective representatives.

1.7 Payment for Demo Equipment . Nano is purchasing the Demo equipment described in Schedule A-1 (the “ Demo Equipment ”) for $1,583,224.66, which the parties hereby agree is the net book value (NBV) thereof as of the Closing Date (the “ Demo Equipment Purchase Price ”). Nano shall pay for such equipment in the manner described in this Section. After the outstanding balance of the Purchased Inventory Purchase Price shall have been reduced to zero pursuant to Section 1.6 of this Agreement, then within ten (10) days after the end of the month in which Nano receives payment on the sale by Nano of each Automated Interferometer System, Nano shall pay to Zygo an amount equal to the price paid to Nano by Nano’s customer for such system, to be applied toward the price of the Demo Equipment, until the Demo Equipment Purchase Price shall have been paid in full. For example, if, after the Purchased Inventory Purchase Price shall have been reduced to zero pursuant to Section 1.6 of this Agreement, Nano sells an Automated Interferometer System for $1,200,000 and the outstanding balance of the Demo Equipment Purchase Price exceeds $1,200,000 at the time of such sale, then Nano shall pay to Zygo the amount of $1,200,000 within ten (10) days after the end of the month in which Nano receives payment of $1,200,000 from Nano’s customer, and such $1,200,000 shall be applied toward the outstanding balance of the Demo Equipment Purchase Price.

1.8 […*…].

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1.9 Full Payment of Acquired Assets . Notwithstanding the provisions of Sections 1.6 and 1.7 above or any other provision of this Agreement, full payment by Nano to Zygo for the Purchased Inventory Purchase Price and Demo Equipment Purchase Price shall be completed (paid in full) no later than ten (10) business days after the first anniversary of the Closing.

ARTICLE II

REPRESENTATIONS AND WARRANTIES OF ZYGO

Zygo represents and warrants to Nano that the statements contained in this Article II are true and correct as of the date of this Agreement, except to the extent such representations and warranties are specifically made as of a particular date (in which case such representations and warranties will be true and correct as of such date).

The Disclosure Schedule attached hereto as Exhibit C is arranged in sections and subsections corresponding to the numbered and lettered sections and subsections contained in this Article II. The disclosures in any section or subsection of the Disclosure Schedule will qualify the corresponding section or subsection in this Article II and any other sections or subsections to which their applicability is reasonably apparent. For purposes of this Article II, the phrase “to the knowledge of Zygo” or any phrase of similar import shall be deemed to refer to the actual knowledge (without independent inquiry or investigation) of the Key Persons.

2.1 Organization, Qualification and Corporate Power . Zygo is a corporation duly organized, validly existing and in corporate and tax good standing under the laws of the State of Delaware and has all requisite corporate power and authority to carry on the Business and to own and use the properties owned and used by it in the Business. Zygo is qualified to do business and is in corporate and tax good standing in the state of Oregon.

2.2 Authorization of Transaction . Zygo has all requisite power and authority to execute and deliver this Agreement and the Ancillary Documents and to perform its obligations hereunder and thereunder. The execution and delivery by Zygo of this Agreement and the Ancillary Documents, the performance by Zygo of this Agreement and the Ancillary Documents and the consummation by Zygo of the transactions contemplated hereby and thereby have been duly and validly authorized by all necessary corporate action on the part of Zygo. Each of this Agreement and the Ancillary Documents has been duly and validly executed and delivered by Zygo and constitutes a valid and binding obligation of Zygo, enforceable against Zygo in accordance with its terms, except as enforceability may be limited by (a) applicable bankruptcy, insolvency, reorganization, fraudulent transfer, moratorium or similar laws in effect from time to time affecting creditors’ rights generally, and (b) general principles of law or equity.

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2.3 Noncontravention . Neither the execution and delivery by Zygo of this Agreement and the Ancillary Documents, nor the consummation by Zygo of the transactions contemplated hereby or thereby, will (a) conflict with or violate any provision of the Certificate of Incorporation or by-laws of Zygo, (b) except for required filings with the Securities and Exchange Commission, or other public company filings, require on the part of Zygo any notice to or filing with, or any permit, authorization, consent or approval of, any Governmental Entity, (c) conflict with, result in a breach of, constitute (with or without due notice or lapse of time or both) a default under, result in the acceleration of obligations under, create in any party the right to terminate, modify or cancel, or require any notice, consent or waiver under, any contract or instrument to which Zygo is a party or by which Zygo is bound, or (d) result in the imposition of any Security Interest upon any Acquired Assets, except, in all instances of (b), (c) and (d) above, for (i) any conflict, breach, default, acceleration, termination, modification or cancellation which would not adversely affect the consummation of the transactions contemplated hereby or (ii) any notice, consent or waiver the absence of which would not adversely affect the consummation of the transactions contemplated hereby.

2.4 Ownership and Condition of Acquired Assets .

(a) Zygo is the true and lawful owner, and has good title to, all of the Acquired Assets, free and clear of all Security Interests. Upon execution and delivery by Zygo to Nano of the instruments of conveyance referred to above, Nano will receive the Acquired Assets, free and clear of all Security Interests, except as provided in Section 1.4(b)(iv) hereof.

(b) Each tangible Acquired Asset listed on Schedule A-1 is free from material defects, has been maintained in accordance with normal industry practice, is in good operating condition and repair (subject to normal wear and tear) and is suitable for the purposes for which it presently is used.

(c) Schedule A-1 lists individually all Acquired Assets which are Demo Equipment, indicating the cost, accumulated book depreciation (if any) and the net book value of each such fixed asset as of the Closing Date.

2.5 Intellectual Property . None of the Acquired Assets infringes, misappropriates or otherwise violates any patent, copyright, mask work right, trademark right, trade dress right, trade secret right, or other intellectual property right of any Person. The use, sale, export and import of such Acquired Assets do not infringe or misappropriate any intellectual property rights of any Person. Zygo makes the representations and warranties in this Section only as to the Acquired Assets that have not been modified in any way after delivery to Nano hereunder where the modification causes any claimed infringement.

2.6 Inventory . All inventory included in the Acquired Assets consists of a quality and quantity usable and saleable in the ordinary course of business, except for obsolete items and items of below standard quality which are identified in Section 2.6 of Exhibit C .

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2.7 Contracts . Zygo has delivered to Nano a complete and accurate copy of each of the Assigned Contracts. With respect to each Assigned Contract: (i) the agreement is legal, valid, binding and enforceable and in full force and effect; (ii) subject to obtaining the consent contemplated by Section 4.6 hereof, the agreement is assignable by Zygo to Nano and will continue to be legal, valid, binding and enforceable and in full force and effect immediately following the Closing in accordance with the terms thereof as in effect immediately prior to the Closing; and (iii) neither Zygo nor, to the knowledge of Zygo, any other party, is in material breach or violation of, or default under, any such agreement, and no event has occurred, is pending or, to the knowledge of Zygo, is threatened, which, after the giving of notice, with lapse of time, or otherwise, would constitute a material breach or default by Zygo or, to the knowledge of Zygo, any other party under such agreement.

2.8 Litigation . There is no Legal Proceeding which is pending or, to Zygo’s knowledge, has been threatened against Zygo related to the Business or the Acquired Assets. There are no judgments, orders or decrees outstanding against Zygo related to the Business or the Acquired Assets.

2.9 Warranties . No product or service manufactured, sold, leased, licensed or delivered by Zygo, the obligation of which is being assumed by Nano, in connection with the Business is subject to any guaranty, warranty, right of return, right of credit or other indemnity other than (i) the applicable standard terms and conditions of sale or lease of Zygo, which are set forth in the Assigned Contracts, and (ii) manufacturers’ warranties for which Zygo has no liability.

2.10 Employees . Section 2.10 of Exhibit C contains a list of all employees (and their status of citizenship) of Zygo whose services relate primarily to the Business. To the knowledge of Zygo, no employee or group of employees listed on Schedule 4.4 hereto has informed Zygo that such employee(s) plan not to accept employment with Nano if so offered by Nano. Zygo is not a party to or bound by any collective bargaining agreement, and has not experienced any strikes, grievances, claims of unfair labor practices or other collective bargaining disputes that relate to the Acquired Assets or the employees of Zygo listed on Schedule 4.4 hereto. Zygo has no knowledge of any organizational effort made or threatened, either currently or within the past two years, by or on behalf of any labor union with respect to the employees of Zygo listed on Schedule 4.4 hereto.

2.11 Legal Compliance . Zygo is currently conducting, and has at all times in the past two years conducted, the Business in compliance with each applicable law (including rules and regulations thereunder) of any federal, state, local or foreign government, or any Governmental Entity, except for any violations or defaults that, individually or in the aggregate, have not had and would not reasonably be expected to be materially adverse to the Business as a whole. To Zygo’s knowledge, it has not received any notice or communication from any Governmental Entity alleging noncompliance with any applicable law, rule or regulation related to the Business.

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2.12 Customers and Suppliers . Section 2.12 of Exhibit C sets forth a list of each supplier that is the sole supplier of any significant product or service to Zygo related to the Business. Section 2.12 also sets forth a list of each customer of the Business, and each party with whom Zygo has engaged over the past twelve months as a prospective customer of the Business, including a summary description of the status of such engagement. To Zygo’s knowledge, no such customer or supplier has indicated within the past year that it will stop, or decrease the rate of, buying products or supplying products, as applicable, to Zygo. No purchase order or commitment of Zygo which is an Assigned Contract was in excess of normal requirements at the time entered into.

2.13 Permits . To Zygo’s knowledge, there are no material permits, licenses, rights, registrations or other authorizations (collectively, “ Permits ”) required in connection with Zygo’s conduct of the Business. Notwithstanding the foregoing, Nano’s sole recourse with respect to a breach of this representation shall be fulfillment of Zygo’s obligations under Section 4.12 hereof.

2.14 Brokers’ Fees . Zygo has no liability or obligation to pay any fees or commissions to any broker, finder or agent with respect to the transactions contemplated by this Agreement.

2.15 Fixed Assets . Section 2.15 of Exhibit C sets forth a list or description of all fixed assets located in the Oregon Facility that are the subject of the Sublease Agreement. There are no liens on such fixed assets, other than customary landlord’s liens.

2.16 Lease for the Oregon Facility . Attached as Section 2.16 of Exhibit C is a true and correct copy of Zygo’s lease of the Oregon Facility (the “ Lease ”). Zygo has paid all amounts due to date under the Lease and has performed all obligations of Zygo required to date under the Lease.

ARTICLE III

REPRESENTATIONS AND WARRANTIES OF NANO

Nano represents and warrants to Zygo that the statements contained in this Article III are true and correct as of the date of this Agreement.

3.1 Organization and Corporate Power . Nano is a corporation duly organized, validly existing and in good standing under the laws of the State of Delaware. Nano has all requisite corporate power and authority to carry on the businesses in which it is engaged and to own and use the properties owned and used by it.

3.2 Authorization of the Transaction . Nano has all requisite power and authority to execute and deliver this Agreement and the Ancillary Documents and to perform its obligations hereunder and thereunder. The execution and delivery by Nano of this Agreement and the

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Ancillary Documents and the consummation by Nano of the transactions contemplated hereby and thereby have been duly and validly authorized by all necessary corporate action on the part of Nano. This Agreement has been duly and validly executed and delivered by Nano and constitutes a valid and binding obligation of Nano, enforceable against it in accordance with its terms, except as enforceability may be limited by (a) applicable bankruptcy, insolvency, reorganization, fraudulent transfer, moratorium or similar laws in effect from time to time affecting creditors’ rights generally, and (b) general principles of law or equity.

3.3 Noncontravention . Neither the execution and delivery by Nano of this Agreement or the Ancillary Documents, nor the consummation by Nano of the transactions contemplated hereby or thereby, will (a) conflict with or violate any provision of the Certificate of Incorporation or by-laws of Nano, (b) except for required filings with the Securities and Exchange Commission, or other public company filings, require on the part of Nano any filing with, or permit, authorization, consent or approval of, any Governmental Entity, (c) conflict with, result in breach of, constitute (with or without due notice or lapse of time or both) a default under, result in the acceleration of obligations under, create in any party any right to terminate, modify or cancel, or require any notice, consent or waiver under, any contract or instrument to which Nano is a party or by which it is bound or to which any of its assets is subject, except for (i) any conflict, breach, default, acceleration, termination, modification or cancellation which would not adversely affect the consummation of the transactions contemplated hereby or (ii) any notice, consent or waiver the absence of which would not adversely affect the consummation of the transactions contemplated hereby, or (d) violate any order, writ, injunction, decree, statute, rule or regulation applicable to Nano or any of its properties or assets.

3.4 Use of Technology . In addition to selling the Zygo Unifire system, Nano is entering into this Agreement and the Supply Agreement with the current intention of using commercially reasonable efforts to market and sell all four types of systems enumerated as clauses (a) through (d) in the definition of “Approved Systems.”

3.5 Viability . To Nano’s knowledge, it has sufficient resources, financial and otherwise, to satisfy each of its obligations hereunder and under the Supply Agreement as each comes due.

ARTICLE IV

COVENANTS

4.1 Proprietary Information . From and after the Closing, neither Party shall disclose or make use of (except to pursue its rights under this Agreement or the Ancillary Documents), and each Party shall use its best efforts to cause all of its Affiliates or other advisors or representatives not to disclose or make use of, any knowledge, information or documents of a confidential nature or not generally known to the public with respect to Acquired Assets, the Business or the other Party or its business (including the financial information, technical

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information or data relating to its products and names of its customers), except to the extent that such knowledge, information or documents shall have become public knowledge other than through improper disclosure by such Party or an Affiliate or other advisor or representative thereof. Notwithstanding the foregoing, nothing in this Agreement shall be construed to prevent Zygo or Nano from making its required filings with the Securities and Exchange Commission, or other public company fili