I was withheld SSn and Medicare tax for 2005 year. I asked my employer to refund the amount but my employer was unable to proide refund. I filed my taxes using 1040 filing as single and I am Indian citizen. Later I filed amended return to file Married filing jointly using 1040X. I then sent IRS 8843 claiming for SSN and Medicare refund but I was refused since I filed 1040. I understand that I can claim my wife as dependent since I am indian citizen. If I sent IRS another 1040X, 1040 NR, 8843 am I still eligible for standard deduction 10000 and 6400 for married filing jointly or does it change.

Please advise.

Thanks...

If you are an F1 student in 2005, then you must file nonresident tax return. On the nonresident tax return, you can get standard deduction (only your own) as per tax treaty and exemption for your spouse (but no standard deduction for spouse). Your income is not subject to FICA taxes.

But you filed resident tax return in 2005. That is why you can not get FICA taxes back. If you file amended tax return, you can not get standard deduction of $10,000. Where did you get this figure? Do some reading or consult a tax professional.
Read: U.S. India tax treaty for students Your U.S. Tax Return: U.S. Tax Treaties for Students and Apprentices
Read nonresident tax filing: Your U.S. Tax Return: U.S. Tax Filing Requirements for Non-Residents

Your first step is to amend your tax return for 2005, filing Form 1040NR with the Form 1040X and printing the word "AMENDED" at the top of the first page of Form 1040NR.

You must make it clear on the Form 1040X that you were NOT LEGALLY ALLOWED to file jointly with your wife in 2005. Expect to pay some additional tax.

Once that amendment is accepted, then (and only then) can you re-filed the Form 843 to try to get the Social Security and Medicare taxes back.

If you need professional help to do this, email me at the email address below.