I have been used F1 for 7 years, and then transferred to H1-b for academic for 4 years. I filed my tax with 1040 form since 2000. My H1-b was changed from academic to industry last year on October and I don't have working permission in states from Jan to Sep in 2008. I went back to my country and work for the company as a contractor for two months with 30% federal tax withholding from the paycheck . I start ed work on Oct, 2008 with H1-b in the company. I already filed my W-2 form with 1040, and just received 1042-S form on Apr 24, which I didn't file it earlier. Do I need to file the 1042-s income to my 1040 form? If I do, where do I put the income and withholding federal tax? Do I need to refile the state tax? Also, will I been charged for the plenty for passing the deadline?
Thanks
Appreciate your help
Cathy Lin

I'm not sure I understand fully your question. It is possible to get both a F W-2 and a F 1042s, based on the type of income you receive.

Many international students receive both form 1042-S and form W-2 The F1042S is used
however, to report income only to a nonresident aliens.

It seems like your filing as a resident as you say you're filing 1040, (NRA file F1040NR/EZ)
So I question if you're a resident or NRA or both during the year, or the from 1042s should not have been issued to you in the first place.

If you in fact were both a resident and a nonresident in the same year you should file as a dual status alien, ( i.e. two returns on as a NRA and one as a resident)
see pub 54.

So you may need to do some research.

If for whatever reason you left income off your federal tax return that should have added, certainly you should add it.

Not including income that's reportable is inviolation of US tax law.

In order to add income left off, complete F1040X, the US Amended Tax return used to make corrections. The income left off goes on line 1. column b, and added appropriately in column c. Your federal income tax withheld goes on line 11, same procedure. You must complete the full front page however, ( report your orignal figues in column a), also complete part 2 on the back.

You can be charged penalties, and also interest if you owe a balance, like you would on your original return if tis paid late. Penalties can "possibly" be waived by attaching a penalty waiver statement to your return, or to the penalty notice if received.

Most State returns have a reciprocal amended return procedure, I would refer you to your state tax instructions or state tax dept.
on that matter.

If you got 1042-S for contractor income, then you will report it on schedule C or C-EZ. You can deduct your business related expenses. On the net income you will pay 15.3% SE tax.
Tax withheld will appear on the same line as W2 tax withheld.