The NTFS file system has metadata - 11 files in all that get created when an NTFS volume is formatted. Basically, they contain information about the other files on the drive - that is, the data files. If you want to learn more specifics about the NTFS metadata, you can find various articles on the web, including one here from Windowsnetworking.com.
For today, rather than get into all the specifics of these files, I wanted to give a brief overview of how PerfectDisk handles metadata. In summary, PerfectDisk defragments all of the NTFS metadata files. You can see a list of these files in PerfectDisk by clicking on the Excluded Files tab in the Statistics window that appears after a partition analysis. PerfectDisk defragments all of these during the offline (boot time) defrag.
Why should you care? It goes back really to PerfectDisk doing all it can to completely defragment your drives. Since the metadata are files, it stands to reason that if they are fragmented, you have more fragmentation on your drive. Other defragmenters do not defragment these files (with the exception of the MFT). Even more interesting, other defragmenters do not report to the user that these files are not defragmented! Which I guess makes sense - sometimes if there is no good news to tell, the philosophy is not to tell anything. But this leads to misinformation - you can get a report showing that there are no fragments when there really are. Don't ask, don't tell, I suppose...
If you want to defragment all the metadata, which is part of defragmenting your entire drive, use PerfectDisk. Nothing else will do it.