I came to US in August 2002 to do PhD at Iowa State University and graduated in March 2007, all the time on F-1 Visa. From March to October 2007, I was on OPT as a post-docotral researcher at University of Wiscosin-Madison. From October 15th 2007 to December 2007 I was on H1-B visa, as a post-doctoral researcher at University of Wiscosin-Madison. In 2007, both Iowa state and University of Wisconsin have deducted social security and medicare taxes for the whole 2007. Can I file my 2007 tax return as a non-resident to claim back social security and medicare taxes?

No you will not get back the FICA taxes.
You have already completed 5 years on F1/OPT. For 2007, you will file a resident tax return.