I am a F1 student since 2003. Have been working at a company since September '09 with OPT(Optional Practical Training). I filed a regular tax filing for the year 2009. I just found ou that while I was on OPT I didn't have to pay the SS and Medicare. Got the money refunded through my employer for the tax that was deducted for Medicare and SS for this year(2010). My employer is now asking me to file the Tax Amendment form(1040X) with IRS to get the amount I paid in 2009 for SS and Medicare(after Sept '09, when I worked with under my OPT).
Also, I had filed for my income from my previous employer before I started working with my OPT and already got the refunds.
Can I file for the tax refund for SS and Medicare after Sept '09? Is 1040X the form to use? Will IRS come back and ask about my income while on F1?

You do NOT file Form 1040X to get a refund of FICA (Social Security and Medicare) taxes.

The forms that need to be submitted are Forms 843 and 8316. This is a separate process than submitting your annual tax return.

If you need professional help completing and submitting these forms, email me at [email protected] for details and a fee quote.