Lately I tried to remove some streams from MKV file - I wanted: video, audio in my language and no subtitles. I achieved it with mkvtoolnix utils.
Firstly I have to identify streams in file:
$ mkvmerge -i input_file.mkv File 'test.mkv': container: Matroska Track ID 0: video (V_MPEG4/ISO/AVC) Track ID 1: audio (A_DTS) Track ID 2: audio (A_AC3) Track ID 3: audio (A_DTS) Track ID 4: audio (A_AC3) Track ID 5: subtitles (S_TEXT/UTF8) Track ID 6: subtitles (S_TEXT/UTF8) Chapters: 16 entries
You could use more verbose tool mkvinfo for that purpose too.
Now we know what to do next:
$ mkvmerge -o out.mkv -d 0 --audio-tracks 2 --no-subtitles input_file.mkv mkvmerge v6.3.0 ('You can't stop me!') built on Jun 29 2013 11:48:33 'test.mkv': Using the demultiplexer for the format 'Matroska'. 'test.mkv' track 0: Using the output module for the format 'AVC/h.264'. 'test.mkv' track 2: Using the output module for the format 'AC3'. The file 'out.mkv' has been opened for writing. Progress: 100% The cue entries (the index) are being written... Muxing took 3 minutes 10 seconds.
This is the fastest way - no need for conversion of any stream.