That's what happened to me last year. Got a letter from the IRS asking why I filed 1040 EZ instead of 1040 NR-EZ.  They asked for details on how I paid for school, asked me for my I-20 and other details. I had to file a 1040X (amendment form). I guess its luck when it comes to you getting audited. I was unlucky but I know a lot of people who file online and haven't got in any trouble. The only drawback is that the interest rate that the IRX charges for back taxes on such issues is usually higher than what most credit card companies would charge.  So might find yourself paying the IRS some boku bucks!!!

I think once you are here for over 5 yrs, you can apply online( i.e; as a citizen would).