Hi Hareesh, 

Since most colleges in Maharashtra depend on the MHT-CET to give out their seats, you may find it tough to find a college that gives you a government college that gives you a seat based on your JEE merit. 

However, some colleges in Maharashtra do accept students based on their JEE Main score, such as the Government college of engineering, Aurangabad and Visvesvaraya National Institute of Technology, Nagpur. 

However most colleges that consider the JEE main score are private Universities, such as Symbiosis, MIT Pune, etc. 

With a private University you may have a better chance of getting a branch you desire, however you can apply to government Universities through your JEE Main rank as well.