There are many tutorials on youtube regarding the process of “transcoding” Canon movie files for use in Final Cut timelines. All of the Canon camera’s use a similar (if not identical) format, so you can usually consult editing tutorials for the 7d or 60d. We must transcode the MOV files that come from the the Canon T3i because they are stored using the h264 codec. These files are too heavily compressed for the typical editing computer to easily handle. Thus, Apple has produced several “intermediate” codecs like AIC (for older Macs) or Prores422 (for newer faster machines). This video should give you a good idea of how to process your files. Remember to make a backup copy of your original Canon files and store them somewhere safe.
Another method of transcoding your files is featured here along with a discussion of converting 720p60 footage for slowmotion effects: