Social security & medicare tax was not withheld from my paycheck because I have J1 Visa. I do meet the IRS presence test to file as a resident. Does me not paying social security taxes prohibit me from filing as resident. Or the using residency when filing income tax return is only for income tax purposes only, so I can still do it (file as resident)?

Since you are under a J-1 visa, the time in the United States under that J-1 visa does NOT count toward the Substantial Presence Test.

For this reason, you will file as a non-resident alien, filing Form 1040NR or 1040NR-EZ plus Form 8843 plus the state tax return.

If you need professional help filing your return, email me at [email protected].