What is the best subject for doing an M.Tech in Manipal Institute of Technology?

The choice of subjects for doing an MTech depends on your inclinations and also your engineering background. In my opinion, the best bet would be Microelectronics or digital electronics and communication. 

• The intake for Microelectronics is limited so your rank needs to be pretty good to increase chances of selection. The intake is more for other branches. 
• The Subjects also almost remain the same with a variation of three subjects and labs. 
• Microelectronics students will be working on cadence and verilog whereas Digital Electronics and Communication students will be working with Matlab. You have the freedom to learn both.

Additionally, there is a branch called the School of Information Science (SOIS) that offers a degree equivalent to an MTech degree which is MS. Its course is at or with industrial trends. The overall curriculum focuses more on lab work than theoretical knowledge. The courses offered here are embedded systems and VLSI digital electronics.

In all, MS offers a better hands-on experience but MTech is a better choice if you want to pursue teaching.