So I've never encountered this problem before, but I'm trying to edit some video that came off of a camera that encodes everything as a .mov file and final cut pro doesn't recognize .mov files. Is there an easy way to encode these to something else?
I don't actually have Final Cut, but I'd be amazed if it can't open .mov files. Can you open the files in QuickTime Player? I'm guessing that it's using a codec that you don't have.
If it's .mov, then it will almost certainly be encoded in MPEG-2 or H264, both of which FCP will handle. However, neither of those is an editing codec, and requires a lot of cpu time to decode. Because of this, you should transcode them to AIC or ProRes using QuickTime Pro, MPEG Streamclip or Compressor.
You -may- also need to install something like the Perian QuickTime component to get them to play, but probably not.