Medical Electronics Engineering Technology is a broader field of study that appeals to aspirants desiring to be technological, and, at the same time, dedicate their careers to saving lives by helping physicians and nurses in their treatment process and patients as well who are suffering from various kinds of ailments. Aspirants can study postgraduate and research programs in Medical Electronics Engineering. Many Universities all over the globe offer the course. On completion of the course, aspirants can look out for career in Government agencies and also in private sector. Most of Medical Electronics Engineers work in health cares, research laboratories, and medical institutes and so on.
Biotechnology Engineering:
Biotechnology is a rapidlydeveloping field. Many private businesses are exploring this field and heavily investing in it. It is safe to say that there are ample job opportunities for B.E./B.Tech. Biotechnology Graduates in private sector.Government sectortoo offers job opportunities, but not in the scale in which private sector does. Average starting salary is generally between 2.4 to 5 Lakh Rupees per year.

Hello aspirant!!
Both of the branches are good and have large scope in future but your college also matters a lot.
Normally,biotech is mostly related natural biology and it also have subjects related to that while in medical electronics engineering have greater attached electronics parts so I think second will be better option for you.
Good luck!!