Hi, I think am in the same trouble of filling wrong tax forms. I filed 1040 online instead of 1040NR for 2008.I started my training job on J1 visa in July 2008. I was told that I would be considered a non resident alien for 2008 and 2009. So should I correct my 2008taxes now before filing for 2009. How many weeks it usually takes. For 2008, Me and my wife filed as "married filing jointly" as she had a work permit as J2 dependent, though she didn't work. I did not pay any social security or medicare taxes for 6 months in 2008 and entire 2009. I started paying them back from 2010. Any answers that would guide me correcting my mistake will be kindly appreciated.

On J-1 and J-2 you are nonresident for two years and do not pay SS tax and Medicare Tax.
Residents pay these taxes. You filed resident return and did not pay SS tax and Medicare tax.

You filed resident tax return for 2008, which was a mistake. You may file amended tax return Form 1040X along with properly done non-resident tax return and Form 8843. You will get deduction as per tax treaty. Pay the tax due. Attach a letter for Waiver of Penalty giving your reasons this happened.
Your spouse will file only Form 8843 if she did not have income more than $3650.
Your U.S. Tax Return: U.S. Tax Filing Requirements for Non-Residents (http://taxipay.blogspot.com/2008/03/us-tax-filing-requirements-for-non.html)