I've been working since June'08 on OPT. I got my H1 this year and have been on H1 since Oct 1st 2008. No Social Security or Medicare Taxes have been withheld. I understand the taxes need to be deducted for period between Oct 1st to Dec 31st 2008. I received my W-2 couple of days back and emailed my employer just today and am waiting for the response. What should be done by me now? What form should I be using? Is it 1040 NR- EZ or 1040 EZ? Also do I need to wait for the amount to be deducted and get a new W-2 or can I file with the existing one?

You need do nothing more.

By emailing your employer about the error of him NOT withholding Social Security and Medicare taxes from 1 Oct 08 onward, you have met your legal responsibility in this matter. Any further actions MUST be taken by the employer; it is now out of your hands.

You do NOT have to wait for a new W-2 to file your federal or state income tax returns.

As for your federal tax return, I assume that you are NOT married. If so, then file Forms 1040NR-EZ and 8843 one last time. You have not met the SUbstantial Presence Test and are therefore NOT required to file a dual-status return.

You CAN file dual-status if you are willing to wait until early June 2009 to file, but there is like NO TAX ADVANTAGE in doing so, so why wait?