I have been in the U.S. since aug 2004 with a F1 visa, same for my wife. Both of us are from Peru. Since sept 2006 we are working with our OPTs.

In 2004 we filed a 1040NR and in 2005 a 1040 (with TurboTax). My understanding is that there is no problem with our 2005 1040 form because the presence test. I am right? I was thinking to file 2006 as alien resident.

Also she has been exempted for the social security and medicare in her work, but not me. If I want to apply for a refund in social security and medicare taxes, does it matters that I filed the past year as a resident alien? Or do I have to make a correction for last year, file this year as NR and the apply for the refund? Or I can apply for my refund independently of my federal and state taxes status?

Thanks in advance for your help

No, there IS a problem.

In 2005, you were STILL non-resident aliens (the time spent in the U.S. while on F-1 visas does not count towards the Substantial Presence Test). You need to amend that return with Form 1040X and attach a correctly-prepared Form 1040NR for yourself. Your wife needs to do the same thing. The IRS may NOT accept the amendment because, normally, filing jointly is an IRREVOCABLE decision, but you need to try because, right now, you have filed incrrectly for 2005 and this MAY affect any future attempt to gain permanent residency status.

Until you get it resolved, you cannot file either a form 843 to request a refund of Social Security and Meicare taxes, nor can you file your 2006 tax return (because you do not know whether to file as a resident or non-resident alien.