I joined university as a reasearcher on H1B June 13, 2006. According to tax treaty, I am exempted from federal and state tax for 3 years (June 13, 2006-June, 2009). So I am a non-resident alien and should file form 1040NR, right? Many thanks.

No. You will still be a resident if you pass the SPT. However, you will be able to claim the treaty exemption on your 1040.

Also, this year you will be a dual status alien and thus file a dual status return.

Handle with care - see Pub 519.

Much depends on the country from which you came.

What IS that country?