Well, I actually suck at this kind of things, but I'll try to answer. I'll tell you what I do in this case. You'll need avisynth and VirtualDub. You can download both of this here: http://www.animemusicvideos.org/members/files.php
, they're in AMVapp. Make sure to download this package, it's very useful. And you might also need, Haali Media Splitter(a.k.a. MatroskaSplitter. Download here: http://haali.su/mkv/
). Install those programs and then here's what you need to do: create a new avisynth script, by pressing right button on the desktop and choosing New>avisynth script, open it and write this:
DSS2("put here the location of your file(e.g. C:), then this symbol "\"and then the name of your file")
So if I have an mkv file named anime, located on D disk, then I would write like this DSS2("D:\anime.mkv"). Then you can import this file to VirtualDub. The go to Video>Compression and choose any codec you like. I think Lagarith should do(you can find this codec in AMVapp), but if not use another one... Personally I use Premiere and After Effects and I cna import avisynth scripts directly into those programs, cause I installed PremiereAVSPlugin(Also from AMVapp). Then press F7 to export your file form VirtualDub and you can start editing. You cna also working a bit on your file inside of VirtualDub to get it ready for editing even better(adjusting frame size, frame rate, etc.), but I don't really know it well. I'm sure there are lots of tuts on this site about all of this.
I think that's it. Hope this will be helpful, if any questions, feel free to ask. But use PM. Thanks for attention, bye.