www.makemkv.com

I own a passive 3D setup by Infitec. The Infitec system is a dual 1080P projector setup. It is a passive 3D Dual Projector solution. What I want is to play 3D movies that are NOT .iso. I know that .iso is the best quality solution (full blu-ray 3D) but I want to be able to play my 3D movies on the non-commercial 3D software player Media Player Classic - Home Cinema. (If you want the reason why I want to play my 3D movies on MPC-HC: MPC-HC can use madVR as output renderer and madVR can read 3DLUT files). The problem is that MPC-HC does not support frame-packed 3D .iso. So I was wondering if makeMKV is a way to rip my 3D .iso's to a format that is supported by MPC-HC + madVR wihout losing ANY resolution/quality.

MakeMKV is going to give you the same resolution as the BD itself, because it doesn't recode the video. The issue is whether or not your software/hardware player can play MVC 3D video from within an MKV file, or if it supports doing so from M2TS files (what you get if you use MakeMKV's "backup" mode). Such support is rather skimpy right now.