hi,
I filed 1040EZ for year 2005 under F1 visa and filed 1040EZ for year 2006 under OPT.
I also filed forms with IRS to claim back the ss & medicare, however, they told me filed 1040EZ indicates that I am a resident of the United States and as a resident of the United States, I am not exempt from FICA tax.

does that mean I have to file form 1040NR first and also file 1040X?

thanks a lot!

On F1/OPT you are exempt from residency for 5-years, and you can only file nonresident tax return.

You filed resident tax return. On resident tax return you get standard deduction, which is not available to nonresidents. Nonresidents get deduction as per tax treaty. Residents pay FICA taxes; only nonresidents don't pay FICA taxes.

Yes, if you want FICA taxes, you must amend your tax return. You will file Form 1040X with your nonresident tax return. May be you will owe some taxes on your nonresident tax return. Then you must pay it with interest and penalty.

Read about FICA taxes and filing Form 843 for refund: Your U.S. Tax Return: Social Security and Medicare (FICA) Taxes for Non-resident Exempt Individual (http://taxipay.blogspot.com/2008/03/non-resident-exempt-individual-social.html)