Dear Sir,

Just one more concern in my case. I filed 1040EZ before and selected the option marriage filling jointly. Since my wife is also on F1 status, we both have to file 1040X separately or combined?
With 1040EZ we received around $1500, but now when I checked with 1040NR-EZ, I suppose to receive around $800. That means I received extra 700. Should I also send the check of this amount with 1040X, or first wait for their response and then do as they suggest?

You have a problem, because the IRS will NOT allow you to revoke the joint filing decision, even if you filed incorrectly.

So, what should I do now?

As I said in my email, you SHOULD try to amend the return, because the way you filed (joint return with your wife) was an incorrect return due to your visa status.

However, the IRS has, in the past, taken the position that filing jointly us a decision WHICH CANNOT BE REVOKED and

And that IRS position trumps all other considerations.

So your amendment, even though it is correct, proper and valid, very likely will NOT be accepted.