I completed my Msc with Applied Physics Can I apply for ISRO exam and whats are the subject??

Yes of course you can join ISRO after MSc in Physics. And you can follow following steps. 

First finish your BSc and MSc with first division/65% marks/6.5 CGPA on a scale of 10.
There exists ISRO Centralised Recruitment Board (ICRB) which conducts an entrance exam. 
Log on to ISRO's website and look for Vacancies/Recruitment option and check for any position of interest.
Register for the exam.
Look at the pattern of previous year papers and prepare well.
Once selected, you will get a call for an interview.
Clear the interview.
Join ISRO.