first, you will need to identify tracks:
$ mkvmerge -i file.mkv
File 'file.mkv': container: Matroska
Track ID 1: video (V_MPEG4/ISO/AVC)
Track ID 2: audio (A_AC3)
Track ID 3: audio (A_AC3)
Then extract audio track you need;
$mkvmerge -o d9.makv -d 1 --audio-tracks 3 file.mkv
mkvmerge v2.9.8 ('C'est le bon') built on Aug 15 2009 01:36:32
'file.mkv': Using the Matroska demultiplexer.
'file.mkv' track 1: Using the MPEG-4 part 10 (AVC) video output module.
'file.mkv' track 3: Using the AC3 output module.
The file 'd9.mkv' has been opened for writing.
The cue entries (the index) are being written...
Muxing took 81 seconds.
and that's all - we copied file and kept only single audio track and single video track :)