Soham Sinha asked me to answer this question.
It has been very long since I applied, but, if I remember correctly many top colleges do not accept application for masters if you already have a master's degree. I cannot go through the website of each college to find it out for you. (Philosophically speaking, I can, but I don't want to.)
But, some colleges do accept application for masters even if you already have a masters. The easiest way to find this out would be to contact the secretary for graduate students of the department you want to apply to via email. They are usually very good at answering questions of students. If you don't receive a response within 3-4 days, you can also call them on phone. They should be able to help you out.
Anyway, I don't think it is a good idea to do what you are trying to achieve. B.Tech. profile will matter as much now as it will later when you apply to top universities. Moreover, you will likely have to provide your own funding if you apply for Masters as most schools don't have funding for MS students. Sometimes, even Ph.D. students were unfunded in my department in MN.
Good luck Samyak Datta.
I like to blog about various topics ranging from education in IITs to social issues in India and US. All opinions and views presented here are my own and not of my employer.