For the first half of 2006 I worked in the university while on my F1 visa. From September 2006 I started working in a private company while on my OPT status. I believe I will get two W2 from both employers. What are the forms that I should complete to get all the due refunds?
Thanks

You should still file as a non-resident alien, using Form 1040NR or 1040NR-EZ, for the federal tax return.

File as a normal state resident for the state tax returns.

Your university income almost for sure is NOT subject to Social Security and Medicare taxes; the same probably applies for the OPT. If, however, the OPT company did withhold these taxes, you need to ask for a refund. If they refused (and they will), file Form 843 with the support forms specified on page 46 of IRS Pub 519.