Here’s a better description than I was able to post on Twitter of how to use ffmpeg to remux MKV (Matroska) files into MP4 files for playback on Apple TV, iOS devices, etc. Since you’re not actually converting the H264 video inside the MKV, it should be extremely fast.

The setup isn’t that hard if you have any kind of basic understanding of how to do stuff in Terminal.

Step 1

Get the appropriate ffmpeg binary from this site:http://ffmpegmac.net

Unzip that badboy and copy it into /usr/local/bin/ (handy hint for GUI lovers — in Finder, just do a ⇧⌘G and open the folder up, then drag your unzipped ffmpeg file in)

Step 2

Fix the permissions and ownership of the file by doing this:

sudo chown root:wheel /usr/local/bin/ffmpeg
sudo chmod 755 /usr/local/bin/ffmpeg

Step 3

Almost done. Just go to the directory where your video file is stored in Terminal and run this command:

ffmpeg -i inputfilename.mkv -acodec copy -vcodec copy outputfilename.mp4

Some MKVs may require some tweaking of the command line options but I’ll leave it to you and Google to figure that out.