SEC Form 4

FORM 4		UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 STATEMENT OF CHANGES IN BENEFICIAL OWNERSHIP Filed pursuant to Section 16(a) of the Securities Exchange Act of 1934 or Section 30(h) of the Investment Company Act of 1940	OMB APPROVAL OMB Number: 3235-0287 Estimated average burden hours per response: 0.5
X	Check this box if no longer subject to Section 16. Form 4 or Form 5 obligations may continue. See Instruction 1(b).

1. Name and Address of Reporting Person* Perez A Carlos (Last) (First) (Middle) 1240 DEMING WAY (Street) MADISON WI 53717 (City) (State) (Zip)	2. Issuer Name and Ticker or Trading Symbol TomoTherapy Inc [ TOMO ]	5. Relationship of Reporting Person(s) to Issuer (Check all applicable) X Director 10% Owner Officer (give title below) Other (specify below)
	3. Date of Earliest Transaction (Month/Day/Year) 06/10/2011
	4. If Amendment, Date of Original Filed (Month/Day/Year)	6. Individual or Joint/Group Filing (Check Applicable Line) X Form filed by One Reporting Person Form filed by More than One Reporting Person

Table I - Non-Derivative Securities Acquired, Disposed of, or Beneficially Owned
1. Title of Security (Instr. 3)	2. Transaction Date (Month/Day/Year)	2A. Deemed Execution Date, if any (Month/Day/Year)	3. Transaction Code (Instr. 8)		4. Securities Acquired (A) or Disposed Of (D) (Instr. 3, 4 and 5)			5. Amount of Securities Beneficially Owned Following Reported Transaction(s) (Instr. 3 and 4)	6. Ownership Form: Direct (D) or Indirect (I) (Instr. 4)	7. Nature of Indirect Beneficial Ownership (Instr. 4)
			Code	V	Amount	(A) or (D)	Price
Common Stock	06/10/2011		D		80,500	D	(1)	0	D

Table II - Derivative Securities Acquired, Disposed of, or Beneficially Owned (e.g., puts, calls, warrants, options, convertible securities)
1. Title of Derivative Security (Instr. 3)	2. Conversion or Exercise Price of Derivative Security	3. Transaction Date (Month/Day/Year)	3A. Deemed Execution Date, if any (Month/Day/Year)	4. Transaction Code (Instr. 8)		5. Number of Derivative Securities Acquired (A) or Disposed of (D) (Instr. 3, 4 and 5)		6. Date Exercisable and Expiration Date (Month/Day/Year)		7. Title and Amount of Securities Underlying Derivative Security (Instr. 3 and 4)		8. Price of Derivative Security (Instr. 5)	9. Number of derivative Securities Beneficially Owned Following Reported Transaction(s) (Instr. 4)	10. Ownership Form: Direct (D) or Indirect (I) (Instr. 4)	11. Nature of Indirect Beneficial Ownership (Instr. 4)
				Code	V	(A)	(D)	Date Exercisable	Expiration Date	Title	Amount or Number of Shares
Stock Option (right to buy)	$3.46	06/10/2011		D			36,400	(2)	11/17/2011	Common Stock	36,400	(2)	0	D

Explanation of Responses:

1. Disposed of pursuant to the Agreement and Plan of Merger dated as of March 6, 2011 (the "Merger Agreement") among Accuray Incorporated ("Accuray"), Jaguar Acquisition, Inc. and TomoTherapy Incorporated ("TomoTherapy"), in exchange for a combination of $253,575.00 in cash and 13,266 shares of Accuray common stock based on $3.15 per share and 0.1648 shares of Accuray Common Stock for each TomoTherapy share held.

2. These options vested over a four-year period, with 13,600 shares vesting on 11/17/05, 13,600 shares vesting on 11/17/06, 13,600 shares vesting on 11/17/07, and 13,600 shares vesting on 11/17/08. These stock options were cancelled and exchanged for 22,378 new stock options of Accuray with the same vesting terms, based on a conversion ratio of 0.6148, which is (A)(i) $3.15 divided by (ii) $7.00, the volume weighted average of the daily closing price of Accuray for the five (5) consecutive trading days preceding and including June 9, 2011, plus (B) 0.1648 pursuant to the Merger Agreement, at a new exercise price of $5.63, based on the previous exercise price divided by the same conversion ratio.

Remarks:

	/s/ Carlos A. Perez	06/13/2011
	** Signature of Reporting Person	Date
Reminder: Report on a separate line for each class of securities beneficially owned directly or indirectly.
* If the form is filed by more than one reporting person, see Instruction 4 (b)(v).
** Intentional misstatements or omissions of facts constitute Federal Criminal Violations See 18 U.S.C. 1001 and 15 U.S.C. 78ff(a).
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