Hi, I am a J-1 research scholar from India who started a position in the US in 2014. I was expecting to go back in two years, so I took advantage of the US/India tax treaty and therefore did not have to pay taxes for 2014 and 2015. However, I've ended up overstaying the 2 year limit and now need to pay taxes for 2014 and 2015. (2016 taxes were deducted by my employer so I have a "regular" return for this year.)

My question is whether I owe an interest/penalty for the 2014 and 2015 taxes? And if so, how do I calculate this? Would it be possible to request a waiver? How is this done? Do I just write a letter to the IRS and attach it to the tax return?

Just to confirm, is it correct that I now need to recompute my taxes for 2014 and 2015 using the 1040NREZ and submit this along with 1040X, and a check for taxes owed?

Amend your 2014 and 2015 return using Form 1040X and attaching Form 1040NR-EZ with the word "AMENDED" written on the top. Send the forms with a check for each year. USE SEPARATE ENVELOPES! Sending two returns in one envelope is a good way to get one of the returns lost!

On the Form 1040X, explain WHY you are amending and ask that they waive all penalties and interest. The INTEREST will probably NOT be waived, but the penalties probably WILL be waived. Let the IRS do the calculations and bill you.

Thank you very much, AtlantaTaxExpert.

A quick follow-up question. Should I use the IRS website to pay the tax due or is it better to send a check along with a 1040-V and the other forms? Is there a separate form I'll need to attach in case I make the payment online?

I believe the check with the voucher is the best option; it certainly is the cheapest, because paying with a credit card involves a convenience fee of at least 2%.