Well, you can try MakeMKV, and it's free while still beta, which it has been for quite some time now. I've found it to be unreliable when main movie spans multiple m2ts files. This quite apart from the fact that it lags behind in coping with new master key block (MKB) and BD+ protections, as compared to AnyDVDHD and DVDFab/DVDFabPasskey.
Typically, I extract main movie this way: Run a driver-level decrypter in the background (like AnyDVDHD or DVDFabPasskey). Extract main movie from disc with Clown_BD (an eac3to front-end). If your decrypter is up to date, Clown_BD is utterly reliable in extracting main movie. It will also correct any problems with the lossless audio track such as sync byte discontinuities if you re-encode to AC3.
Then I backup main movie to BD25 using BDRebuilder and store the original disc away. For making MKVs, I use Ripbot, but Handbrake is similar, and both use the x264 encoder; presets are somewhat different. If you extracted all subtitles in the first step, Ripbot can identify any forced subs embedded in the subtitle (pgs) streams, and you can hardsub them into the picture if you want. This will require a re-encode, but if you use quality-based encoding and a crf (constant reference factor) value of 16-18, the result should be very nearly indistinguishable from the original. The lower the crf value, the nearer to the original in quality, and original file size, the output will be. Or you can simply select copy stream for both audio and video and repackage to MKV. Chapter timings will be preserved.
The particular container you use depends on what your hardware requires, but MKV should be fine. I use MKV because the inbuilt media player on my TV recognizes that container when playing videos directly from a 2 TB powered, ntfs formatted, external hard drive. (I have a couple).
There's more than one way to do this, but that's one way.