I have secured rank 7 in AIIMS Msc biotechnology and rank 1 in AIIMS Msc Reproductive biology and clinical embryology. I am confused regarding the choice of subject. Which subject should i choose ? Which one has better scope in future. ?

Congratulations!!
Reproductive biology and clinical embryology: In The practicals of this course you will be doing some of those which are performed in Msc Biotechnology.As a Clinical Embryologist you can work in an IVF Clinic alongside a Gynaecologist and an Urologist. But the Pay scale isquite less: 3 to 4 lakhs per annum maximum it can go to 6- 8 lakhs.
MSc biotechnology is also complete research based course. You will have to go for pHD, work as a research fellow as JRF student or their are various private companies in R&D like Norvartis etc which hire biotechnologists