Physics

IISC Bangalore
Indian Institute of Astrophysics Bangalore
Inter University Centre for Astronomy and Astrophysics Pune
Harish Chandra Research Institute Allahabad
Satyendranath Bose National Center of Basic Sciences Kolkata
Saha INSTITUTE of Nuclear Physics Kolkata
Institute of Mathematical Sciences Chennai Mathematical Institute Chennai
Institute of Physics Bhuvaneshwar
Institute of Plasma Research Gandhi Nagar
Inter University Accelerator Center Delhi
Tata Institute of Fundamental Research Mumbai
Raman Research Institute Hyderabad
Most of these post graduate studies take place and the entry is through Joint Entrance Screening Test (JEST) or by clearing NET JRF and getting a direct call for interview.

Hi Ashfaque, well, there are basically two ways to study in India either by self-financing or on scholarships provided. Indian embassy offers scholarships to a lot number of Nepalese students. The exam is quite easier if you are from Madesh or educationally underprivileged district classified by GoN. Some of the great colleges where you can study on self financing are VIT, MIT Manipal, MIT Pune, DTU, NITs, CFTIs etc. For DTU, NITs, CFTIs, you have to apply through DASA scheme. You have to appear in SAT subject tests and get selected. For colleges like VIT etc, you can get admission directly subject to eligibility criteria. In this case, you don't need any help from embassy as you don't need a visa to go to India.
Footnote: If I were you, for biotechnology I would choose NITs, DTU, CFTIs rather than colleges like VIT etc. If I have to study in some local and non-reputed college, I would not go to India. I would rather study in Kathmandu University whose B. Tech in biotechnology is highly recognized and offers a good career.