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To correct a 941 Quarterly Federal Tax Return that has already been processed by the eFile Center, file the Form 941-X (Adjusted Employer’s Quarterly Federal Tax Return) or Claim for Refund.
Note: To see if the 941 Return has been processed by the eFile Center, refer to: Filing Status
Form 941-X is a stand-alone form corresponding to, and relates line-by-line with, the employment tax return it is correcting. The employer is able to file Form 941-X when an error is discovered on the original form.
Visit the following link to read more about Form 941-X:
http://www.irs.gov/instructions/i941x/ch01.html#d0e188
You may print the 941-X form and mail it to the IRS. At this time, the IRS does not have a means to accept electronically filed 941-X forms.