How do I get rid of Longhorn Directories

I ran longhorn beta for a while to test for microsoft, and now i have a lot of crap on my drive after reinstalling XP. I went for broke and all longhorn and ran it for a few weeks, then reformatted now having hidden problems. Longhorn reformatted my Trig Drive to FS files and I am using RAID config with SCSI, and NTFS XP. Problems have shown themselves after i rewiped the SCSI drives and reinstalled XP. Has anyone had this problem?