I haven't looked at this for years, but if the Windows file-system is not fundamentally different from what it was in the good'ol days of floppy disks and DOS, you need to do a low level read of the sectors where the directory and file structure is kept and then for each file traverse the linked lists which map the clusters where the data is stored and somehow calculate the amount of dispersion of the files over the disk.

All pretty ugly stuff at a low level and most certainly ideal to totally mess up your disks.