Hi,
I am a first year graduate student on my F-1 VISA at Chicago. I work as a teaching assistant here. I filled my first years tax return FORM 1040, using FreeTaxUSA software, and did not fill FORM 1040 NR. I read only recently that non-residents need to fill in FORM 1040 NR and not FORM 1040. Will there be any problem or any negative repercussions to my future application of VISAs?:(
Abir Bhattacharjee.

You should amend your return. Fill out form 1040X and a complete non-resident alien return (form 1040NR or 1040NR-EZ as well as form 8843).
http://www.irs.gov/pub/irs-pdf/f1040x.pdf
http://www.irs.gov/pub/irs-pdf/f1040nr.pdf
http://www.irs.gov/pub/irs-pdf/f1040nre.pdf
http://www.irs.gov/pub/irs-pdf/f8843.pdf

As long as you correct your honest mistake, there are no repercussions.

I agree; the return does need to be amended, but it is a honest (and all too common) mistake, so the IRS will take no punitive actions.