mkv is a container format not an encoding scheme just like avi is a container format
matroska is just a format for multiplexing the audio and video together that is open source
use a matroska demuxing program to separate the tracks and then you can do whatever you want..........problem most run into when trying to convert to something else is the video is often h264 or some variation and not many converters will do that
or you can use a player like mplayer to literally output each stream to a file instead of your screen using command line options