Hello. I'm in a huge mess! I've been an international student since 2008. For 2008, I filed form 8843 because I didn't work. For 2009 and 2010, I worked and paid medicare, social security, state, FICA, and federal taxes. I only got refunded for state and federal taxes. I didn't file form 8843 because I thought form 1040 was enough. I filed as a resident.
What can I do to fix this?

FIRST, you must amend the returns for 2009 and 2010, filing Form 1040X and asking that your non-resident alien status be re-instated. You will attach properly-prepared Forms 1040NR-EZ and 8843 to the Form 1040X, while printing "AMENDED" to the top of the first page of the Form 1040NR-EZ. It is likely that you owe added taxes, so send the amendment in with checks.

SECOND, contact your employer and ask for a refund of the FICA taxes for 2009 and 2010. The IRS REQUIRES that you attempt to get the money back from the employer. If they refuses (likely given the time that has passed), ask for a refusal letter on company letter, one for each year, that states HOW MUCH was paid in FICA taxes and WHY thety cannot refund the money. The refusal leter, though NOT absolutely necessary, makes the Form 843/8316 process go much faster.

Once the IRS acknowledges receipt of and processes these amendments, then (and ONLY then) can you request a refund of the FICA (Social Security and Medicare) taxes that were improperly withheld form your salary for 2009 and 2010 by submitting Form 843 and 8316. The refusal letter cited above makes the processing go faster, but it will still take about six months to get your refund.

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