Dear candidate, hope you are doing well.

Yes you are eligible to opt mtech in cse. Even the candidates having specialisation with CSE can get admitted into IITs for CSE. You just need to score a good score for the admission process. There are top IITs like Bombay, Madras, Kanpur, Delhi providing good faculty and infrastructure for Mtech.

Check out the link below for getting more information about the top colleges

Hope this helps.