Following this procedure will save you lots of time and prevent video quality degradation if you need video in mp4 format for playback through iTunes, the Apple TV, or your iOS device.
Download MP4Tools from here and copy the application to your Applications folder.
Launch MP4Tools from your Applications folder.
Click Open, select your mkv file, and click Open again.
Ensure that your video and audio tracks are selected. If your video is H.264 you will not need to re-encode the video so select Pass Thru from the video section. If the audio is aac you will not need to re-encode the audio so you can select Pass Thru from the audio section. If it is NOT aac then select AAC from the audio section.
Click convert to begin creating your MP4 file.