You can - we do too. We found that the timer job that rebuilds indexes only rebuilds an index once it becomes 30% fragmented. It never does any sort of reorganization and this became an issue with some of the larger tables since 30% of the fragmentation would be 10s of GB.

If you Google "sharepoint index defrag" you'll get a lot of good information - including what steps you need to do to replace it with your own.