i hav done BE in biomedical field. i have applied for MTech in Embedded Systems Design program at International Institute of Infotrmation Technology,Pune (IsquareIT) with colaboration with IGNOU-Indhira gandhi National Open Unibversity. Should i go ahead? I am confused

Yes of course dear, there is nothing to worry about it. Just go for it, there is nothing to think of it. IIIT,pune is one of the reputed institutes of India and also a Institute of National Importance and its colaboration with IGNOU now guanrantees u best quality of education.