I'm on F1 visa (non-resident alien) and my spouse is on H-1B visa (resident alien). We are looking at filing our taxes as Married filing jointly. My social security and medicare taxes were withheld. 1)Can I file for the refund of social security taxes withheld erroneously? Would I be treated as a non-resident for the exemption of FICA taxes? 2)Is the process for refund the same, i.e. filling form 843 ?

You can file joint return as residents. If you file joint return, you will not get FICA taxes back.

Or your spouse files as married filing separately and you file nonresident tax return. Then you can file Form 843 to get back FICA taxes. Your U.S. Tax Return: Social Security and Medicare (FICA) Taxes for Non-resident Exempt Individual

@MukatA, I would like your opinion on this particulat FICA issue. The following IRS link says that Nnon-resident spouse can file jointly with RA and still be exempted from FICA taxes.

http://www.irs.gov/businesses/small/international/article/0, id=96370,00.html

"If, at the end of your tax year, you are married and one spouse is a U.S. citizen or a resident alien and the other spouse is a nonresident alien, you can choose to treat the nonresident spouse as a U.S. resident. This includes situations in which one spouse is a nonresident alien at the beginning of the tax year, but a resident alien at the end of the year, and the other spouse is a nonresident alien at the end of the year.

If you make this choice, you and your spouse are treated as residents for your entire tax year for the purpose of your federal individual income tax return, and for the purpose of withholding U.S. federal income tax from your wages. However, for the purpose of Chapter 3 withholding you may still be treated as a nonresident alien. Refer to Withholding of Tax on Nonresident Aliens and Foreign Corporations (Chapter 3 of the Internal Revenue Code) in Tax Withholding Types. In addition, you may still be treated as a nonresident alien for the purpose of withholding Social Security and Medicare tax. Refer to Aliens Employed in the U.S. – Social Security Taxes"