For tax year 2007 got a w-2 for wages also a 1099 for bonuses and another for mileage and gas reimbursement. Reported both 1099's on line 21 now IRS wants me to fill out a schedule C and a SE. I am not self employed, so schedule C will not work and the long form of SE does not apply. Any help would be appreciated.

You must report 1099-misc income on schedule C or C-EZ (Form 1040). You can deduct your business related expenses directly on schedule C or C-EZ. Net income is subject to SE tax at 15.4%.
On your W2 income employer paid their share of SE taxes at 6.2% + 1.45%. They also deducted it from your wages at 7.65%. Now on bonus, who will pay these taxes?
Read: How you will treat the 1099-Misc income, read: Your U.S. Tax Return: W2 vs 1099-Misc: Employee vs Independent Contractor.

Yo MAY be able to convince the IRS that Schedules C and SE do not apply if you can get documentation from your employer stating that the Form 1099 income is for mileage and gas reimbursement.

As for the bonus, that SHOULD have been included on the W-2. In my opinion, Schedules C and SE ARE required there.

Thank you both for your answers, apparently I put the 1099 income on the wrong line which notified IRS something strange going on. I know you can not convince IRS if your life depended on it. I now know what a diservice my employer is doing to me. But hopefully my new CPA can fix it with a minimum "ouch"

You will need to get your employer to re-issue the Form 1099s in order to get the IRS to change their stance.

Good luck!

The employer should have reported this on Form W2. If on W2 it is reported as wages, then you will take deduction for employee business expenses, which is itemized deduction.

This is from the instructions to Form 1099-Misc, page Misc -5, column 2:
"Exceptions. Do not report in box 7, nor elsewhere on Form 1099-Misc, the cost of current life insurance protection (report on Form W-2 or Form 1099-R), an employee's wages, travel or auto allowance, or bonuses (report on W-2), or the cost of group-term life insurance paid on behalf of a former employee (report on Form W-2)."

If the employer is not willing to amend form 1099-misc, you will report it on schedule C. Deduct all your actual expenses on schedule C. Only balance amount, if any, is your taxable income subject to SE tax.

MukatA has a point.

If you HAVE to report the mileage and gas reimbursements on Schedule C, then, logically, you can deduct the COSTS of the mileage and gas as well, plus other costs, such as business use of your cell phone.