Pretty sure this has been answered and it's really old, but in case anyone ends up here with the following setup:
-Samsung 3d TV (I think they stopped making them this year
- Plex app on that TV (it *will* play full framed 3D from in m2ts, you just have to get there from the 3D BD)
-------------- Background ------------
I rip, encode, remux on Apple (El Cap) and/or Linux (ubuntu 16.04)
I use MakeMKV, tsmuxergui, Handbrake (GUI and CLI), along with various scripts I've written
My media server is Plex running on the linux machine, with storage of 3TB drives in a raid6. 3 is the sweet spot right now. Lowest $/byte. Why not snapraid? I use extended attribute metadata, since the drives also serve files via netatalk (Apple protocol) and tags and such are saved as extended attributes. Snapraid doesn't support extended attributes right now. There is also a hot spare drive and mdadm monitoring. I've lost (and recovered) RAID5 and lost completely a RAID6 (was not monitoring as 3 drives failed over 6 months). Was all rips/encodes I have originals of so no data lost but a lot of time. Even with stale backups (about 80% of the non-HD stuff), it took months to recover. Worth the extra drive to lower that chance that. And not it's monitored. Heavily :p
My clients are Plex running on OSX, Samsung, IOS, and android. Perpetual Plex Pass from way back (Good software deserves financial support). The latest IOS11 savvy client with PIP in other open apps is awesome. Being able to pick up where I left off any show from anywhere I happen to be (globally) and automagically... way cool. Have been stuck in an ER in another city, watching Kung Fu series from my home server. Watched movies while waiting for a ferry in another country.). I use VLC for local mobile media. Plex sync still doesn't "have it" perfect. Better than a subscription content service. MakeMKV was another one well worth paying for. When I use something and get solid value from it... pay the peeps to help them keep up the good work.
Anyway....
-------------- What I Do -------------------
Step 1: Rip 3D BD using Makemkv. I have added advanced options so everything selects as I want (except the 3D MVC I still have to select by hand. Only for 3D movies, obviously). You end up with a pretty big mkv file. Usually 30-45GB. This won't work (yet) for the Plex client on a Samsung TV. It needs to be m2ts format.
Step 2: Remux with tsmuxergui (a gui for txmuxer, obviously). When I drag and drop the mkv, I get a blank error dialog box, sometimes. Close it and do it again. Dropping it a second time and it's fine. You'll see all the parts. Select m2ts muxing. This will repack the whole thing into a single m2ts file that Plex on Samsung will play in full 3D glory, just fine. You can delete the ripped mkv if you want. Unless you plan on doing something else with it. Like extracting a 2D HD version. Or encoding it to something smaller with handbrake. Oh, and make sure you don't have leftovers in the muxer. If you drag a movie into it while one is still there, it will mux it all together; that's what muxers do. Clear the one movie out before muxing another.
That's it. Two steps. This is a solution that works with 3d BD plying on Samsung 3DTV, using the Plex App for Samsung, *not* using Plex on a PC hooked up via HDMI.
Incidentally, a PS3 does play 3D BD's via HDMI to the same TV. Also have Plex client on Mac mini hooked up to same TV. It does not play 3D files down the HDMI that the Samsung TV can understand.
Cheers,
Anyway, back to whatever I was looking for and/or doing before. OMG, I need some coffee.... break time!