I came to US on an L1 visa on Feb 11th 2006 and left May 3rd 2006. I lived for only 81 days. During this time I earned about 13000 dollars in wages. I am also single. When I apply the substantial presence test, I find I do not pass it. Can someone tell me how I should file the Federal and CT taxes and what forms do I use. When I use the online web sites I think these softwares are treting me to have lived in the US for a whole year.

You would file Form 1040NR or 1040NR-EZ, which CANNOT be filed online.

What about the forms that I need to file CT taxes.

Check out the Connecticut state government webiste for the needed forms. You will need to file as a part-year resident.