I'm trying to figure out the best settings for converting or recoding a mkv file into a mov or mp4 or something after effects will allow me to import.
I've read up a bit about recoding the mkv, it works as a container right? And switching to something else will be the least corruptive way of getting the footage out. What's the best way of doing this and what format settings etc to choose?

I've tried using MKVExtractGUI-2 to do it but it doesn't seem to like me and keeps telling me there are no chapters in the file I'm trying to use.

Another thing is the file is quite big so I was also looking for the best way of extracting sections out, can you do that to pieces when you recode it or do I just do the whole thing?

Thanks very much for any pointers or help.