Hi,
I am a foreign researcher and became resident alien for tax purposes in 2011 (substantial presence test). One of my incomes in 2011 was a postdoc fellowship from my university, which has been reported in box 3 of a 1099-MISC. There is a treaty between my country and the US, including an exception to the saving clause, and the time limit is in 2012. So I want to claim treaty benefits for all my 2011 income.
I read that 1099-MISC income reported on Box 3 should be entered in Line 21 of the 1040. In addition, I read that if I want to claim treaty benefits, I should write the amount in parentheses or with a negative sign on Line 21 + provide a filled 8833 for each treaty income.
Thus, I am wondering how I could at the same time enter the 1099-MISC box 3 income on Line 21 and claim for treaty benefit on the same line.
Note that for each of my 2 additional sources of income, I received a 1042-S. I was thinking of entering the gross incomes reported on those 1042-S on Line 7 of the 1040, and entering them as negative amounts on Line 21 as well.
Also note that for my 3 incomes, NO federal tax has been withheld so far.
Does anyone have any suggestion on how to avoid the mess on Line 21?

For clarity, my main concern is about the income reported on the 1099-MISC box 3 : 1) Where to enter the amount in 1040; 2) how to claim treaty benefit for this income.
Thanks!

Assuming you are from China, you will have to attach a statement showing the 1099 income and the treaty exemption, then showing the net results on Line 21.

Use Form 8833 to explain the exception to the SAVINGS CLAUSE and to claim the treaty exemption itself.