WindowsNT/Windows2000 can use a format called NTFS instead of FAT tables. This renders the disk unreadable to Windows95/98/ME machines.
NTFS=(Windows)NT File System. It can only be read by a system capable of reading NTFS. You cannot normally boot DOS and go to drive C: and read its contents if it is NTFS. NTFS allows windows NT to control access. More than just FAT tables, it also contains permissions and rights filters.
There are drivers to allow you to read and modify an NTFS partition. Win98 NTFS and NTFS for DOS