If you have a "remuxed 3D MKV", you can go to ISO. I'm assuming you used MakeMKV to rip the 3D disc? Get the latest tsMuxeR (v.2.6.12), drag the MKV into it, and choose Blu-ray ISO as the output. That's it, you'll have a movie-only 3D ISO with audio, chapters & subs (whatever you had in the MKV).
The only issue with above is if you have any MVC MKV's with TrueHD. Because TrueHD and core AC3 need to be separate tracks, if you saved only TrueHD, tsMuxeR won't allow you to save to ISO. If you did save the core AC3 separately, you can I believe. In my case, I had to re-rip all my 3D BD's that have TrueHD.