Document:

exv10w45

Exhibit 10.45

AMENDED AND RESTATED EMPLOYMENT AGREEMENT

(CEO)

     THIS AMENDED AND RESTATED EMPLOYMENT AGREEMENT (“Agreement”) is executed as of this 9th day of
March, 2010, by and between TomoTherapy Incorporated, a Wisconsin corporation (the
“Company”), and Frederick A. Robertson, M.D., an individual (“Employee”).

RECITALS

     The Company and Employee entered into an Employment Agreement dated as of November 5, 2008,
which was previously amended by a First Amendment dated as of July 1, 2009 and by a Second
Amendment dated as of October 1, 2009.

     The Company and Employee desire to amend and restate the Employment Agreement to incorporate
the changes made by the First and Second Amendments and to reflect certain other changes agreed to
by the Company and Employee.

     NOW, THEREFORE, in consideration of the premises and the mutual agreements and covenants
contained herein, and for other good and valuable consideration, the receipt and sufficiency of
which is hereby acknowledged by the Company and Employee,

     IT IS HEREBY AGREED AS FOLLOWS:

ARTICLE I

EMPLOYMENT

     1.1 Term of Employment. The Company employs Employee, and Employee accepts employment by
the Company, on the terms and conditions set forth herein for the period commencing on the date set
forth above and ending on March 31, 2011, subject to earlier termination as hereinafter set forth
in Article III (the “Employment Term”). This Agreement shall be automatically extended for
successive additional one-year periods beginning on March 31, 2011 and each subsequent anniversary
thereof (each such extension on a subsequent anniversary of March 31, 2011 an “Extension
Period”) unless, at least 60 days prior to any then current Extension Period, either party
provides the other with a written notice of intention not to renew, in which case Employee’s
employment with the Company, and the Company’s obligations hereunder shall terminate as of the end
of said Extension Period, except to the extent specifically provided herein. The terms of this
Agreement during any Extension Period shall be the same as the terms in effect immediately prior to
such extension, subject to any such changes or modifications as mutually may be agreed between the
parties as evidenced in a written instrument signed by both the Company and Employee.

     1.2 Position and Duties.
Employee is employed in the position of Chief Executive Officer and President and shall be
subject to the authority of, and shall report to, the Company’s Board of Directors. Employee’s
duties and responsibilities shall include all those customarily attendant to the position of Chief
Executive Officer, and such other duties and responsibilities as may be assigned by the Company’s
Board of Directors. Employee shall devote Employee’s
entire business time, loyalty, attention and
energies exclusively to the business interests of the Company while employed by the Company, and
shall perform his duties and responsibilities diligently and to the best of his ability.

ARTICLE II

COMPENSATION AND OTHER BENEFITS

     2.1 Base Salary. The Company shall pay Employee a salary at the annual rate of $450,000
(“Base Salary”), payable in accordance with the normal payroll practices of the Company.

     2.2 Performance Bonus. Employee will be eligible to earn an annual performance based bonus
for that portion of each full calendar year during which Employee is employed by the Company (a
“Bonus Year”), the terms and conditions of which as well as Employee’s entitlement thereto
shall be determined annually in the sole discretion of the Company’s Board of Directors or an
authorized committee thereof (the “Performance Bonus”). Any Performance Bonus payable
hereunder shall be paid following the Bonus Year not later than the earlier of (i) 30 days
following the Company’s receipt of its annual audited financial report or (ii) March 15 of the year
following the Bonus Year.

     2.3 Benefit Plans. Employee will be eligible to participate in the Company’s retirement
plans that are qualified under Section 401(a) of the Internal Revenue Code of 1986, as amended
(“Code”), and in the Company’s welfare benefit plans that are generally applicable to all executive
employees of the Company (the “Plans”), in accordance with the terms and conditions
thereof. The Company intends to provide Employee with: (a) portable term life insurance with a
death benefit equal to twice the sum of Employee’s current Base Salary and target Performance
Bonus; provided, however, that the minimum benefit shall equal at least $500,000; and (b) long-term
disability insurance with an annual benefit equal to at least 75% of the sum of Employee’s Base
Salary and target Performance Bonus. Both the term life insurance and long-term disability
insurance are, however, subject to the underwriting process. To the extent that the costs of such
coverages materially exceed the average of such costs for other executives at the Company, the
Company reserves the right to modify the scope of coverage for Employee, or not offer it at all.

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     2.4 Expenses. The Company shall reimburse Employee for all reasonable expenses incurred in
the course of the performance of Employee’s duties and responsibilities pursuant to this Agreement
and
consistent with the Company’s policies with respect to travel, entertainment and miscellaneous
expenses, and the requirements with respect to the reporting of such expenses.

     2.5 Vacation. Employee shall be entitled to a maximum of four weeks of vacation in any
calendar year in accordance with the Company’s general vacation policies for similarly situated
executive employees.

 ARTICLE III

TERMINATION

     3.1 Right to Terminate; Automatic Termination.

          (a) Termination by Company Without Cause. Since Employee is an at-will employee, subject to
Section 3.2, the Company may terminate Employee’s employment and all of the obligations under this
Agreement at any time and for any reason.

          (b) Termination by Employee for Good Reason. Subject to Section 3.2, Employee may terminate
his employment obligation hereunder for “Good Reason” (as hereinafter defined) if Employee gives
written notice thereof to the Company (which notice shall specify the grounds upon which such
notice is given) within 90 days of the initial occurrence of a “Good Reason” event and the Company
fails, within 90 days of receipt of such notice, to cure or rectify the grounds for such Good
Reason termination set forth in such notice. If the Company fails to so cure or rectify, the
Employee’s termination of employment shall not be deemed for “Good Reason” unless the Employee
terminates employment within one year of the initial occurrence of Good Reason. “Good Reason”
shall mean any of the following: (i) a material reduction of the Employee’s duties and
responsibilities hereunder; (ii) a material adverse change in the working conditions of the
Employee including, without limitation, relocation of Employee’s principal workplace over 50 miles
from the Company’s existing workplace, without the consent of Employee; or (iii) the Company’s
material breach of the Agreement.

          (c) Termination by Company For Cause. Subject to Section 3.2, the Company may terminate
Employee’s employment and all of the Company’s obligations under this Agreement at any time for
“Cause” (as defined below) by giving notice to Employee stating the basis for such termination,
effective immediately upon giving such notice or at such other time thereafter as the Company may
designate. “Cause” shall mean any of the following: (i) Employee has materially breached this
Agreement or any other agreement to which Employee and the Company are parties or has materially
breached any other obligation or duty owed to the Company, which material breach remains uncured
for 30 days after Employee receives notice thereof from the Board of Directors; (ii) Employee has
committed gross negligence, willful misconduct or any material violation of law or the Company’s
Comprehensive Corporate Compliance Program in the performance of Employee’s duties to the Company;
(iii) Employee has engaged in any willful misconduct likely to result in material discredit to or
material loss of business, reputation or goodwill of the Company; (iv) Employee has failed to
follow in any material respect lawful instructions from the officer or body to whom Employee
reports concerning the operations or business of the Company, which material failure to follow
lawful instructions remains uncured for 30 days after Employee
receives notice thereof from the Board of Directors; (v) Employee has been convicted of, or pled
nolo contendere to a felony; (vi) Employee has misappropriated funds or property of the Company; or
(vii) Employee has attempted to obtain a personal profit from any transaction in which the Employee
knows the Company has an interest, and which constitutes a corporate opportunity of the Company or
is adverse to the interests of the Company, unless the transaction was approved in writing by the
Company’s Board of Directors after full disclosure of all details relating to such transaction.
The cessation of employment of Employee shall not be deemed to be for Cause unless and until
there shall have been delivered to Employee a copy of a resolution duly adopted by the affirmative vote
of not less than three-quarters of the independent directors of the Board at a meeting of the Board
called and held for such purpose (after reasonable notice is provided to Employee and Employee is
given an opportunity, together with counsel for Employee, to be heard before the Board), finding
that, in the good faith opinion of the Board, Employee is guilty of the conduct described in this
Section 3.1(c), and specifying the particulars thereof in detail

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          (d) Termination Upon Death or Disability. Subject to Section 3.2, Employee’s employment and
the Company’s obligations under this Agreement shall terminate: (i) automatically, effective
immediately and without any notice being necessary, upon Employee’s death; or (ii) in the event of
the disability of Employee, by the Company giving notice of termination to Employee. For purposes
of this Agreement, “disability” means the inability of Employee, due to a physical or mental
impairment, for 180 days (whether or not consecutive) during any period of 360 days to perform,
with reasonable accommodation, the essential functions of the work contemplated by this Agreement.
In the event of any dispute as to whether Employee is disabled, the matter shall be determined by
the Company’s Board of Directors in consultation with a physician satisfactory to the Company, and
Employee shall cooperate with the efforts to make such determination. Any such determination shall
be conclusive and binding on the parties. Any determination of disability under this Section
3.1(d) is not intended to alter any benefits any party may be entitled to receive under any
long-term disability insurance policy carried by either the Company or Employee with respect to
Employee, which benefits shall be governed solely by the terms of any such insurance policy.
Nothing in this subsection shall be construed as limiting or altering any of Employee’s rights
under state workers compensation laws or state or Federal family and medical leave laws.

          (e) Termination Upon Resignation or Retirement. Since Employee is an at-will
employee, subject to Section 3.2, Employee may terminate employment and all of the obligations
under this Agreement at any time and for any reason. If Employee terminates employment as a
result of retirement from the Company, Employee shall provide the Company with at least 90 days’
notice.

     3.2 Rights Upon Termination; Non-Renewal by Company.

          (a) Section 3.1(a) and 3.1(b) Termination. If Employee’s employment is terminated pursuant
to Section 3.1(a) or 3.1(b) hereof or upon expiration of this Agreement pursuant to the Company’s
notice of its intention not to renew
pursuant to Section 1.1, Employee shall have no further rights against the Company hereunder,
except that the Company, subject to Section 3.2(g), will:

          (i) within 10 days following the termination of employment, pay Employee (a) any unpaid
Base Salary with respect to the period prior to the effective date of termination, (b)
reimbursement of expenses to which Employee is entitled under Section 2.4 hereof, and
payment of any accrued but unused vacation to which Employee is entitled to under Section
2.5 hereof (collectively, the “Accrued Obligations”);

          (ii) subject to Section 3.2(f), pay Employee a lump-sum severance payment (the
“Severance Payment”) 53 days following Employee’s termination of employment, in an amount
equal to the sum of: (a) 2.0 times Employee’s annual base salary as in effect on the date
of termination; and (b) 2.0 times the Employee’s target annual bonus for the year in which
such termination occurs;

          (iii) subject to Section 3.2(f), pay a prorated amount of Employee’s target annual
bonus for the year in which such termination occurs, based on the number of calendar days
elapsed during such year prior to date on which Employee’s termination of employment occurs;

          (iv) subject to Section 3.2(f), pay the COBRA premium for group health care
coverage for Employee and Employee’s eligible dependents, as applicable and to the extent
eligible, provided that Employee properly elects COBRA continuation coverage, for up to
eighteen (18) months immediately following the date of such termination of Employee’s
employment, except that payment of such premiums shall cease if and when the Employee (and
Employee’s eligible dependents) become eligible for medical, hospital and health coverage
under a plan of a subsequent employer; and

          (v) subject to Section 3.2(f), pay up to $10,000 for outplacement services, such
services to be used within two years of termination of employment.

Further, each unvested equity award held by Employee at the time of such termination shall become
immediately and fully vested and each unvested stock option shall become immediately and fully
exercisable and shall not expire before three months after the date on which Employee’s termination
of employment occurs or, if earlier, the expiration of the term of the option.

          (b) Section 3.1(c) and 3.1(e) Termination. If Employee’s employment is terminated pursuant
to Sections 3.1(c) or 3.1(e) hereof, Employee shall have no further rights against the Company
hereunder, except for the right to receive the Accrued Obligations.

          (c) Section 3.1(d) Termination. If Employee’s employment is terminated pursuant to Section
3.1(d) hereof, Employee or Employee’s estate shall have no further rights against the Company
hereunder, except for the right to receive (i) the Accrued Obligations, (ii) payment of the COBRA
premium for group
health care coverage for Employee and Employee’s eligible dependents, as applicable and to the
extent eligible, provided that Employee or Employee’s estate properly elects COBRA continuation
coverage, for up to eighteen (18) months immediately following the date of such termination of
Employee’s employment, and (iii) the continuing rights under the life insurance benefit under
Section 2.3.

          (d) Termination Pursuant to a Change of Control. If, within three (3) months before or
twenty four (24) months following a Change of Control, the Company terminates Employee’s employment
without Cause pursuant to Section 3.1(a), Employee terminates his employment for Good Reason
pursuant to Section 3.1(b), or during such period this Agreement expires following the Company’s
notice of its intention not to renew pursuant to Section 1.1, Employee shall have no further
rights against the Company hereunder, except the Company will, subject to Section 3.2(g):

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          (i) pay the Employee the Accrued Obligations;

          (ii) subject to Section 3.2(f), pay Employee a lump-sum severance payment (the
“Severance Payment”) 53 days following the termination of employment, in an amount equal to
the sum of: (a) 3.0 times Employee’s annual base salary as in effect on the date of
termination; and (b) 3.0 times the greater of (x) the average of the two annual bonuses paid
to Employee for the two years preceding the year in which such termination occurs, provided
that if the Employee was not employed for the period required to be eligible for two prior
annual bonuses, then the amount in this subparagraph (b)(x) shall be the amount of the
annual bonus, if any, received for the year prior to the year in which termination of
employment occurred, or (y) the target bonus for the year in which such termination occurs;
provided such lump sum shall be reduced by the amount of any lump sum payable under Section
3.2(a)(ii);

          (iii) subject to Section 3.2(f), pay Employee a prorated amount of Employee’s target
annual bonus for the year in which such termination occurs, based on the number of calendar
days elapsed during such year prior to date on which Employee’s termination of employment
occur; provided such lump sum amount shall be reduced by the amount of any lump sum payable
under Section 3.2(a)(iii);

          (iv) subject to Section 3.2(f), pay the COBRA premium (and up to the equivalent in cost
to the Company for premiums under an individual plan after COBRA rights expire) for health
care coverage for Employee and Employee’s eligible dependents, as applicable and to the
extent eligible, for the 36 month period immediately following the date of such termination
of Employee’s employment, provided that Employee properly elects COBRA continuation coverage
for the initial 18 months after the date of Employee’s termination and is able to convert to
an individual plan for the remaining 18 months, except that payment of such premiums shall
cease if and when the Employee (and Employee’s eligible dependents) become eligible for
medical, hospital and health coverage under a plan of a subsequent employer, and further
provided such payment shall be reduced by the amount of any payment under Section
3.2(a)(iv); and

          (v) subject to Section 3.2(f), pay up to $10,000 for outplacement services, provided
such payment shall be reduced by the amount of any payment under Section 3.2(a)(v), and
provided further that such services are used within two years of termination of employment.

     Further, each unvested equity award held by Employee at the time of such termination shall
become immediately and fully vested and each unvested stock option shall become immediately and
fully exercisable and shall not expire before three months after the date on which Employee’s
termination of employment occurs or, if earlier, the expiration of the term of the option.

          (e) Definition of Change of Control. As used herein, “Change of Control” shall mean
the occurrence of a “change in the ownership,” a “change in the effective control” or a “change in
the ownership of a substantial portion of the assets” of the Company, as determined in accordance
with this definition. In determining whether an event shall be considered a
“change in the ownership,” a “change in the effective control” or a “change in the ownership of a substantial
portion of the assets” of the Company, the following provisions shall apply:

     (i) A “change in the ownership” of the Company shall occur on the date on which any
one person, or more than one person acting as a group, acquires ownership of stock of the
Company that, together with stock held by such person or group, constitutes more than 50% of
the total fair market value or total voting power of the stock of the Company, as determined
in accordance with Treasury Regulation 

§ 1.409A-3(i)(5)(v). If a person or group is
considered either to own more than 50% of the total fair market value or total voting power
of the stock of the Company, or to have effective control of the Company within the meaning
of part (b) of this definition, and such person or group acquires additional stock of the
Company, the acquisition of additional stock by such person or group shall not be considered
to cause a “change in the ownership” of the Company.

     (ii) A “change in the effective control” of the Company shall occur on either of
the following dates:

     (A) The date on which any one person, or more than one person acting as a
group, acquires (or has acquired during the 12-month period ending on the date of
the most recent acquisition by such person or persons) ownership of stock of the
Company possessing 30% or more of the total voting power of the stock of the
Company, as determined in accordance with Treasury Regulation 

§ 1.409A-3(i)(5)(vi).
If a person or group is considered to possess 30% or more of the total voting power
of the stock of the Company, and such person or group acquires additional stock of
the Company, the acquisition of additional stock by such person or group shall not
be considered to cause a “change in the effective control” of the Company; or

     (B) The date on which a majority of the members of the Company’s Board of
Directors is replaced during any 12-month period by directors whose appointment or
election is not endorsed by a majority of the members of the
Company’s Board of Directors before the date of the appointment or election, as
determined in accordance with Treasury Regulation § 1.409A-3(i)(5)(vi).

     (iii) A “change in the ownership of a substantial portion of the assets” of the
Company shall occur on the date on which any one person, or more than one person acting as a
group, acquires (or has acquired during the 12-month period ending on the date of the most
recent acquisition by such person or persons) assets from the Company that have a total
gross fair market value equal to or more than 40% of the total gross fair market value of
all of the assets of the Company immediately before such acquisition or acquisitions, as
determined in accordance with Treasury Regulation § 1.409A-3(i)(5)(vii). A transfer of
assets shall not be treated as a “change in the ownership of a substantial portion of the
assets” when such transfer is made to an entity that is controlled by the shareholders of
the Company, as determined in accordance with Treasury Regulation § 1.409A-3(i)(5)(vii)(B).

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          (f) Exclusive Remedy; Waiver and Release. To the extent permitted by applicable law, the
payments contemplated by this Section 3.2 shall constitute the exclusive and sole remedy for any
termination of Employee’s employment by the Company (whether pursuant to, or in violation of, the
terms of this Agreement). Employee covenants not to assert or pursue any remedies, other than an
action to enforce the payments due to Employee under this Agreement, at law or in equity, with
respect to any termination of employment, and shall execute a release and waiver on such terms and
conditions as the Company may require as a condition of entitlement to such payments. If any
applicable revocation period for such release and waiver has not expired before the date payment is
due to be made hereunder, such payment shall be forfeited.

          (g) Limitation of Benefits. If any payments or benefits payable to the employee under this
Agreement or otherwise would be subject to the excise tax under Section 4999 of the Code, such
payments and/or benefits will be reduced to the extent necessary so that no amount will be subject
to such excise tax; provided that such reduction will only occur if the employee will be in a more
favorable, after-tax position than if no such reduction was made.

          (h) Six Month Delay. If payment of any amount of “deferred compensation” (as
defined under Section 409A of the Code, after giving effect to the exemptions thereunder) is
triggered by a Separation from Service (as defined in Section 4.7) that occurs while the Employee
is a “specified employee” with respect to the Company (as defined under Section 409A of the Code
and determined in good faith), and if such amount is scheduled to be paid within six (6) months
after such Separation from Service, the amount shall accrue without interest and shall be paid the
first business day after the end of such six-month period, or, if earlier, within 15 days after the
appointment of the personal representative or executor of the Employee’s estate following the
Employee’s death.

ARTICLE IV

GENERAL PROVISIONS

     4.1 Notices. Any and all notices provided for in this Agreement shall be given in writing
and shall be deemed given to a party at the earlier of (i) when actually delivered to such party,
or (ii) when mailed to such party by registered or certified mail (return receipt requested) or
sent to such party by courier, confirmed by receipt, and addressed to such party at the address
designated below for such party as follows (or to such other address for such party as such party
may have substituted by notice pursuant to this Section 4.1):

	 	(a)	 	If to the Company:

TomoTherapy Incorporated
1240
Deming Way

Madison, WI 53717

Attn: General Counsel
	 
	 	(b)	 	If to Employee:

938 Winding Way

Middleton, WI 53562

Attn: Frederick A. Robertson, M.D.

     4.2 Entire Agreement. This Agreement contains the entire understanding and the full and
complete agreement of the parties and supersedes and replaces any prior understandings and
agreements among the parties, with respect to the subject matter hereof., provided that the
Indemnity Agreement dated November 5, 2008, the Confidentiality and Non-Competition Agreement
dated April 1, 2007, (“Confidentiality Agreement”) and the Assignment of Inventions Agreement dated
January 3, 2005, (“Assignment Agreement”) between the Company and the Employee are and shall remain
in effect.

     4.3 Amendment. This Agreement may be altered, amended or modified only in a writing, signed
by both of the parties hereto. Headings included in this Agreement are for convenience only and
are not intended to limit or expand the rights of the parties hereto. References to Sections
herein shall mean sections of the text of this Agreement, unless otherwise indicated.

     4.4 Assignability. This Agreement and the rights and duties set forth herein may not be
assigned by Employee, but may be assigned by the Company, in whole or in part. This Agreement
shall be binding on and inure to the benefit of each party and such party’s respective heirs, legal
representatives, successors and assigns.

     4.5 Severability.
If any court of competent jurisdiction determines that any provision of this Agreement is
invalid or unenforceable, then such invalidity or unenforceability shall have no effect on the
other provisions hereof, which shall remain valid, binding and enforceable and in full force and
effect, and such invalid or unenforceable provision shall be construed in a manner so as to give
the maximum valid and enforceable effect to the intent of the parties expressed therein.

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     4.6 Arbitration. Any controversy, dispute or claim arising out of or relating to this
Agreement (including, but not limited to, any claim regarding the scope or effect of this Section
and any claim that this Section is invalid or unenforceable), or the breach hereof, shall be
settled by a single arbitrator in binding arbitration conducted in Milwaukee, Wisconsin in
accordance with the Commercial Arbitration Rules of the American Arbitration Association (“AAA”)(or
such other arbitration service as the parties may agree upon), and judgment upon the award rendered
by the arbitrator may be entered in any court having jurisdiction thereof. The arbitrator’s
decision shall be in writing. In addition to the Commercial Arbitration Rules of the AAA and
unless otherwise agreed to by the parties, the following rules shall apply:

          (a) Each party shall be entitled to discovery exclusively by the following means: (i) requests
for admission, (ii) requests for production of documents, (iii) up to 15 written interrogatories
(with any subpart to be counted as a separate interrogatory), and (iv) depositions of no more than
six individuals.

          (b) Unless the arbitrator finds that delay is reasonably justified or as otherwise agreed to
by the parties, all discovery shall be completed, and the arbitration hearing shall commence within
five months after the appointment of the arbitrator.

          (c) Unless the arbitrator finds that delay is reasonably justified, the hearing will be
completed, and an award rendered within 30 days of commencement of the hearing.

The arbitrator’s authority shall include the ability to render equitable types of relief and, in
such event, any aforesaid court may enter an order enjoining and/or compelling such actions or
relief ordered or as found by the arbitrator. The arbitrator also shall make a determination
regarding which party’s legal position in any such controversy or claim is the more substantially
correct (the “Prevailing Party”) and the arbitrator shall require the other party to pay the legal
and other professional fees and costs incurred by the Prevailing Party in connection with such
arbitration proceeding and any necessary court action. In addition, the parties expressly agree
that a court of competent jurisdiction may enter a temporary restraining order or an order
enjoining a breach of the Assignment Agreement, the Confidentiality Agreement or any similarly
subsequently executed agreement between the parties, pending a final award or further order by the
arbitrator. Such remedy, however, shall be cumulative and nonexclusive, and shall be in addition
to any other remedy to which the parties may be entitled.

     4.7 Separation from Service. “Separation from Service,” “termination of employment,” or words of similar import shall mean, with respect to any payments of deferred
compensation subject to Section 409A of the Code, the Employee’s “separation from service” as
defined in Section 409A of the Code. For
this purpose, a “separation from service” is deemed to occur on the date that the Company and
the Employee reasonably anticipate that the level of bona fide services the Employee would perform
after the date (whether as an employee or independent contractor) would permanently decrease to a
level that, based on the facts and circumstances would constitute a separation from service;
provided that a decrease to a level that is 50% or more of the average level of bona fide services
provided over the prior 36 months shall not be a Separation from Service, and a decrease to a level
that is 20% or less of the average level of such bona fide services shall be a Separation from
Service. The bona fide services taken into account for purposes of determining whether there has
been a Separation from Service shall be services performed for the Company and any person or entity
that would be considered a single employer with the Company under 

Section 414(b) or 414(c) of the
Code; provided that, in applying Section 1563(a)(1),(2), and (3) of the Code, the language “at
least 50 percent” shall be used instead of “at least 80 percent;” and further provided that “at
least 20 percent” shall be used instead of “at least 50 percent” where based on legitimate business
criteria.

     4.8 Waiver of Breach. The waiver by either party of the breach of any provision of this
Agreement shall not operate or be construed as a waiver of any subsequent breach by either party.

     4.9 Governing Law; Construction. This Agreement shall be governed by the internal laws of
the State of Wisconsin, without regard to any rules of construction concerning the party
responsible for the drafting hereof.

     IN WITNESS WHEREOF, the parties have executed this Agreement as of the day and year written
above.

	 	 	 	 	 	 	 	 	 
	EMPLOYEE:	 	 	 	COMPANY:	 	 
	 
	 	 	 	 	 	 	 	 
	Frederick A. Robertson, M.D.	 	 	 	TomoTherapy Incorporated	 	 
	 
	 	 	 	 	 	 	 	 
	/s/ Frederick A. Robertson

	 	 	 	By:
	 	/s/ A. Sparks-Johnson	 	 
	 

	 	 
	 	 	 	 

	 	 

6exv10w1

Exhibit 10.1

COMMERCIAL VEHICLE GROUP, INC.

2010 BONUS PLAN

Formula for Participants

BONUS = (Salary x BF1 x 70% x BF2) + (Salary x BF1 x 30% x BF3)

Bonus Factor 1 (“BF1”) = the factor awarded to participants in the plan (as a percent of base
salary).

Bonus Factor 2 (“BF2” or “The Company Factor”) represents 70% of the bonus calculation and is based
on EBITDA performance of Commercial Vehicle Group, Inc. for 2010.

The target level payment is based on the company’s business plan for the current year and would
result in a 100% payout. The minimum threshold level for a payout under the 2010 Bonus Plan is
based on the minimum acceptable performance of the company resulting in approximately 75% payout.
The maximum potential payout under the 2010 Bonus Plan is set at approximately 125% payout.
Payments below the minimum threshold or above the maximum potential payout are considered
discretionary and are subject to specific review and approval of the Compensation Committee of the
Board of Directors

Bonus Factor 3 (“BF3” or “The Individual Factor”) makes up the remaining 30% of the bonus
calculation and is independent of the BF2 measurement. Objectives for each position are assigned
and tie to the individual performance of each participant with respect to their specific
responsibilities in support of the overall company goals, including but not limited to: (1) cash
flow, (2) operating and cost reduction initiatives, (3) strategic initiatives, (4) product
development and (5) revenue growth. Such measures are important to the company’s immediate and
long-term objectives, require a significant effort on the individual’s part, and support the
operating and financial targets for the 2010 business plan within each participant’s functional
area.

The Compensation Committee of the Board of Directors reserves the right to review, modify and
approve, at its sole discretion, all BF3 percentages for plan participants.

 

			
	*	 	EBITDA is defined as Earnings Before Interest, Taxes, Depreciation and Amortization. The
Compensation Committee reserves the right to review, modify and approve the final EBITDA
calculation as it relates to the 2010 Bonus Plan for the sole purpose of ensuring that the bonus
payments are calculated with the same intentions for which the targets have been established for
the current year.

Source: [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00170-of-00352.parquet"}, [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00170-of-00352.parquet"}]]