I will be receiving 1099 for contractual work with a company. I being an F-1 OPT student didn't know earlier that they have hired me on those terms. The employment letter states regular consultant-intern role which is like a step before full-time regular employment with market research consulting firms.

Please advice how should I file tax returns. I came to know only recently that F-1 students- non-resident aliens cannot accept employment where they receive 1099.

Another important question:-
Can single F-1 students work as contractors for employers by filling up W-4BEN and filing 1042-S form?

Since you have received, report income on your tax return. 1099-misc income: You are self employed or independent contractor. You will report your income and business related expenses on schedule C or C-EZ (Form 1040). Then you put net income (or loss) on line 12 of Form 1040.
In your case income is not subject to SE tax so do not file schedule SE.

Thanks for your reply.
Does working on contractual basis with 1099 violate F-1 OPT status?

Did you do any violation? If not, why worry.