Clipmark

Then you have to find out which tracks contains the audio and video.
Run:
$ mkvinfo Heroes_S02E11_720p.mkv

Check out the printout to find the tracks.

(in my mkv file video is on track1 and audio is on track 2. Change the numbers to fit you mkv file)

Then demux the mkvfile by running:

$ mkvextract tracks 1:video.h264 2:audio.ac3

Next to do is to change one byte inside the video.h264.
$ hexedit video.h264
On the first line you should see this number combination:
"67 64 00 33"
change this to:
"67 64 00 29"

press ctrl-s to save and ctrl-z to exit

Then you need to convert audio to aac format.
$ mkfifo audiodump.wav
$ neroAacEnc -ignorelength -q 0.20 -if audiodump.wav -of audio.m4a & mplayer audio.ac3 -vc null -vo null -ao pcm:fast

This may take a couple of minutes.

The only thing left is to mux the video and audio file:

$ MP4Box -add video.h264 -add audio.m4a Heroes_S02E11.mp4