Firstly, why are you attempting to defrag? It's seldom necessary on a Mac unless you're creating and deleting very large files frequently (video editing or high-end audio for example).
It's also prone to problems, especially if the application you're using to do it isn't fully up to date for the OS version.
I hope you made a backup before attempting this.
For now, Insert your OS X 10.6 installer disc and restart, holding down the C key at the chime until the Apple logo appears. It will take a few minutes to boot from the disc.
When the installer appears, OK the language page, then ignore the installer and go to the menu bar Utilities menu,
Select Disk Utility.
Select the physical HD in the left pane (top line with the maker's name and size).
Click 'repair disk' (not permissions).
If you get any errors, run the repair again until either you get a green "the volume Macintosh HD seems to be OK" or a message saying the disc can't be repaired.
If the latter occurs, you'll need to try an erase and re-install of OS X (hence the need for the backup).
In future, if you really feel the need to defrag, the safest way to do it is to clone your system to an external drive, which gives you a bootable backup. Boot from the external drive and ensure it works, then use DU from that drive to erase the internal Macintosh HD, then clone the system back to the internal. (Cloning can be done with the Restore function in DU).
That gives you a totally defragged system (both files and free space), plus you still have a backup.
