Hi I am srinivas.I did from my masters from us university and worked on OPT for some time in 2006.When I worked in 2006 my employer gave me 1099-misc instead of W2.As some friends told that on OPT we don't have to pay self employment taxes.I just filed the taxes without paying any self employment taxes(1040).After 1.5 yr now IRS is asking me to pay self employment taxes.I Explained that I am non resident alien for that period.But IRS is not listening to my words.And asking why my employer gave 1099 instead of W2.I don't know what to do.Please advise me if anybody can.

On F1 and OPT you are nonresident for 5-years. Your income is not subject to FICA or SE taxes. You can not file resident tax return. Read this: Your U.S. Tax Return: U.S. Tax Filing Requirements for Non-Residents

Since you have filed resident tax return and claimed standard deduction (instead of deduction under tax treaty, which is still standard deduction), you will pay FICA taxes. Else, file amended returns for all the resident tax return you have filed up to now.