These are instructions on how to convert H.264 MKV files to MP4 without re-encoding using MP4Tools for Mac.
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.
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Full illustrated article: http://www.iclarified.com/entry/index.php?enid=21202
Via Robin Good