A couple quick guides for VirtualDub and AviSynth:http://www.animemusicvideos.org/guides/ ... -vdub.htmlhttp://www.animemusicvideos.org/guides/ ... synth.html
Those are good starting grounds to learn what they are and how to use them. Specifically, on the AviSynth page, it's either DirectShowSource or FFVideoSource that you would look at to open MKV files. You can use DirectShowSource if you can play the MKVs in Windows Media Player, or you can use FFVideoSource if you can't play them in WMP, don't want softsubs to show up in the video stream*, or just prefer to make sure that they're opened in a stable manner (as DirectShowSource has issues with frame accuracy - for basic once-through conversion this isn't a problem, per ce, but it is if you plan on using the script itself in your editing program).
*This is also possible if you use DirectShowSource, but it requires you to disable or otherwise prohibit the subtitles from being shown through VSFilter or ffdshow, whichever one you use to handle subtitles in WMP.