How feasible is it to pursue an M.Tech in computer science from any of the old IITs or premier institutes like IIIT-H and ISI if you are a B.Tech from one of the old IITs in some other discipline, like mechanical or civil engineering?

Apply for Phd instead of M.tech if your sole intention is research. IITs accept students for Phd directly after B.tech, through GATE. Write the exam in any one discipline in which you are sure to get a good rank. Apply to the department of any IIT which offers interdisciplinary research opportunities (research will depend on you area of interest and your guide). Clear the interviews. (FYI cutoff for Phd in CSE is much lower than the cutoff for M.tech but this may not be true for other departments). Even if there isn't any specific interdisciplinary specialization or department, you may chose a guide in one department and a co-guide from another department to help you out in your multidisciplinary research. I would suggest you to talk to some M.tech or Phd student in your college for info about research in other IITs.

M.Tech CS in ISI is indisciplinary... students from backgrounds as diverse as ece, ee, physics, math, stat join the course.... If you crack the entrance/gate cutoff (as declared by ISI) and also ace the interviews... ISI will accept you with open arms. ISI appreciates hardwork & sincerity... she doesn't see which background you are coming from. CHeerio...

Ex IITians ( mech , chem ) are persuing mtech ( 2012 , 2013 batches ) at IIITH. Its quite feasible to get admission for non CSE but after admission you need to do rigorous amount of hard work to satisfy the course requirements. Although I would say you should focus more on MS than MTech if your main purpose is research as research for MTech is only best at IISc which is not to easy to get into.