I rip an iso of my 3D Blu-Rays to my NAS. I then mount and play the 3D iso with either TMNT6 or PowerDVD on my HTPC. AnyDVD was great as I could run it on the HTPC and it would simply block Cinavia detection, not remove it from the source, just block it when it was played.
I'm having trouble finding the least expensive and easiest way to do this now that AnyDVD is no more. I don't care to actually remove Cinavio from the isos, just block it at play time.