To remove unwanted audio and subtitle tracks from Matroska (mkv) files you use mkvtools;
sudo apt-get install mkvtoolnix-gui
Once it is installed then open up the gui (Sound & Video menu) and follow these steps;
1) In the "Input files" box on the "Input" tab browse to the mkv file you want to modify.
2) In the "Tracks, chapters and tags" box uncheck any part you want to remove (leave the stuff you want to keep checked)
3) In the "Output filename" box keep the default name or modify to suit.
4) Click "Start muxing" and wait a minute or two until it completes.
Once you are done, you can delete the original file (after checking it worked of course!) and rename the new file accordingly.