You have to manually file an amended tax return Form 1040-X. Enter your name, address and social security number on the first page of the form. Skip the rest of the form until part III where you enter an explanation as to why you are filing the form. Sign the form. Next, prepare your form 1040NR and attach a signed copy of that return to the amended return. Write "Amended" across the top of the form 1040NR. Enclose a copy of the original form 1040 that you filed and write "Original Return" on the top of it.
Mail the returns to the address listed in the instructions to form 1040-X.
Here is a link to form 1040-X: Form 1040-X
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