Harshil:
You did not start H-1 status early enough to qualify for resident alien status. Unless you want to until June 2006 to file as a resident alien, you must file as a non-resident alien.
You
must file Form 1040NR or 1040NR-EZ and Form 8843 for 2005. For 2006, you will file as a resident alien.
You became liable for Social Security and Medicare taxes the day your H-1 visa became effective. The days prior to that, the withholding of Social Security and Medicare taxes was probably improper. You should be able to file Form 843 to claim a refund for the Social Security and Medicare taxes withheld while on F-1 status. Download IRS Pub 519 from
www.irs.gov and read pages 45-47 for the procedure and documents needed to file this claim.