| Lolnani:
The best way to handle it is for you to file an amended return (Form 1040X). You would attach the Form 1040NR to the Form 1040X. If you owe additional tax, try to get it done before April 15th so no penalties or interest will be due.
If you have filed Form 1040NR/1040NR-EZ in the past, the IRS definitely knows your immigration status, so they may reject the return. In that case, you can then file the Form 1040NR as required. However, I doubt if the IRS will notify you in time to react by the April 15th deadline, so I recommend you be proactive and file the amended return.
Go back to the tax pro who did your original return. Since he made the mistake, he owes you an amended return at no charge. | 
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