Superlazy copy-paste from another forum where someone else asked a similar question.

Imp wrote:
Hi there!
first of all, I doubt there's a "best" method, second thing: there's no easy method.
What I usually do is not getting .mkv files.
but that's not the case here, so let's get working!
what I got and do is the following:
1) I have the following programs:
AviSynth 2.5
AvsPmod
VirtualDub
2) use the AvsPmod to make a script for the MKV, this will be the biggest problem because of MKV being MKV
DirectShowSource("C:\filepath.mkv") or ffvideosource("C:\filepath.mkv") should work,
unless it's not supported, then you need to load a plugin first and that's just hell getting the right plugin
to load a plugin use LoadPlugin("C:\filepath.dll") before the source line
3) save the script.
4) load the script with VirtualDub
5) use the "Save as AVI.??" option under the File menu.
6) if the output video isn't good, play around with the options under the Video menu.
for my editing programs I use the compression Intel IYUV-codec 'i420', and the 'Fast recompress' option
let me be clear, I almost never get what I want out of it.
I clean the footage with my editing programs so no one ever notices.??
I hope this helps, but try to avoid MKVs from now on ^^;
The best of luck with editing!
imp
I pretty much agree with Imp here, except my first and second step are different.
1) I also have MeGui
2) We'll now have MeGui create the script for us.
Open MeGui and load the video into it. (Use the One-Click-Encoder, no need for complicated stuff)
Now run it and wait for it to finish the setup stuff and let it work a bit on re-encoding.
You can break this off after a while (a minute should be plenty)
MeGui will now have created an AviSynth script.
This script will usually contain stuff like deinterlacing, which is pretty unnecessary if you have HD footage, or progressive footage in general so go ahead and remove it. (Will also speed things up a bit later)
After that I do the same thing Imp does. (I use the UT-video codec tho, since it's apparently better for HD footage)
Also, all the programs we have been discussing can be found in the amv-app:
http://www.animemusicvideos.org/guides/ ??? mvapp.html (for some reason the link failed here, but its in the "guide to all things audio and video" )