You can defrag them if they are fragmented. Use a safe defrag utility like Diskeeper '09 which is fast and efficient, and does not grind away at the drive for longer than necessary. Run a disk cleanup and then run Diskeeper to avoid defragging temp files. You can grab free trial versions of Diskeeper from their website.
BTW, it's not a good idea to use the external drive as you would use an internal IDE/SATA drive. Those things are meant mostly for archiving/backups and not continuous long term use. They can begin to run hot quite quickly.