What tax form to use is dependent based on your visa status in the United States not by what you work as. If you are in F1 visa and worked as a research assistant, you should file 1040NR EZ.

How much you would pay in back taxes also dependent upon your tax liability for those years vs how much you paid then. You will have to pay penalty and interest on those back taxes. We don't know your income; we don't know your tax liability; we don't know how much you paid in taxes; we don't know whether you are going to amend your prior returns or just filing a correct and new form for year 2009.

Basically what I am saying is without the full information of everything, it is very hard to tell you how much back taxes you will be paying. Usually the difference between filing a 1040 and 1040NR -EZ is that you don't get to deduct standard deduction ($5700 for 2009) if you file 1040NR EZ. You will be paying additional taxes on the amount that you would deduct as standard deduction. If you have deducted other expenses such as tuition fee to arrive at your AGI, that is not also permitted. 

I hope this helps a little bit.