I am wondering if you could give me best direction in my tax matter.
I am from India. I came to US in June 2008 on J-1 visa for postdoctoral research. Initially I thought, I would stay for less than 2 years. So, I took the tax treaty between US and India which exempts me to pay any tax. I filed the 2008 tax return, in which I didn't owe any tax (according to the treaty). However, at the time of filing 2009 tax return, I decided to extend my stay beyond two years, so I paid off the amount I owe for 2009 tax. ( I did not take the treaty for 2009.)
At that time I had very obscure knowledge about the tax system, and even after inquiry, I did not get a clear understanding. Now I understand that I need to pay off the 2008 taxes also, but I was unable to get a correct advice about this. Do I have to file an amended tax return? Do I have to pay any penalty and/or interest? Since it was not known to me that I'd stay more than 2 years, at the time of filing 2008 taxes, can this be a valid reason to ask for penalty/interest waiver? I have been delaying this all these days, in anticipation of getting correct advice.
Thanks in advance for your advice.

Yes, as per tax treaty the exemption is lost for 2008. So you need to pay the taxes. You will pay interest on the tax amount you owe.
For waiver of penalty, you can attach a request stating your reasons.