It’s really not recommended to use original files from your DSLR in Apple Final Cut Pro. You will notice some performance problems if you try to do so.

The best way to convert your files is to use MPEG Streamclip – a free tool from Squared 5.

After starting it, press -> File -> Export to QuickTime – and in the following screenshot you’ll see my settings:

(click for high res picture)

You should save them on your computer as a preset. So you will never forget them…