How To Convert Anime Discs to MKV files

Converting raw BluRay directory to MKV

Open MakeMKV and pick the index.bdmv file.
Once MakeMKV has opened the directory, choose the Title that matches (Usually the largest) then set output folder and click the Make MKV icon.
Open MKVToolNix and move the file that MakeMKV created into it.
Switch to Output tab and on Splitting change Split Mode to Before Chapters and put the chapter numbers where the episodes change as a comma separated list in Chapter numbers input. Example: 3,6,9
Switch to Input tab and set output folder and then click Start multiplexing
Verify all the files exist and start at proper position. If this is the case, you have successfully converted the Bluray directory to MKV files. ✔