Hi,

I am a French postdoc that arrived in the US in Nov 2007. Until Nov 2009 I was under the tax treaty exemption meaning that my University started to withhold taxes in Nov 2009 (my FICA and medical taxes started in Jan 2009).
I am wondering how to fill my tax return since I want to claim that tax treaty and that my status changed from non resident to resident for this year. Should I fill the 1040NR with the amount that was not subject to withholding and then a 1040R with the taxes for the 2 months Nov-Dec ?
Thanks for any kind of help.

You will file as a non-resident alien, because the time under the J-1 visa does NOT count for the Substantial Presence Test (SPT).

Hence, you have NOT YET met the SPT for 2009, requring you file as a non-resident alien, filing Form 1040NR and Form 8843.