I do not know whether to file 1040 or 1040NR. Here are my details:
I entered US in August 2003 and in the last 5 years I have been outside of US only for a total of 2 months (Dec 2005-Jan 2006). This means I am resident alien for tax purpose and I have to file 1040, right? However last year from Jan to June 2008, I was a full-time student with a fellowship. So I got 1042S. Now if I file 1040 then where do I enter the 'income/tax withheld' information from 1042S? Do I file 1040NR even when I meet the substantial presence test for 2008?
Thanks for your help.

Are you a U.S. citizen or resident? If not, which visa do you have since 2003.

I am neither US citizen nor resident. I am in OPT right now and till June 2008, I was in F1 visa.
May be I didn't explain properly in the last post. So again, I was in school till June 2008 and I also had a fellowship so I got 1042S. However since I have been in US for more than 5 yrs and meet the substantial presence test don't I need to file 1040 (and not 1040NR)?

You will file resident tax return. Include 1042-S income on the line where you enter W2 income. Same about taxes withheld.