I'd run a disk check (go in My Computer, Rightclick on the drive, select "properties", then go in the "tools" tab, the first in that list is the disk check button, after you clicked on it tick both boxes in the popup, then off you go).
Isn't the first time something like that (endless nested folders too long to be deleted) is detected as filesystem error and gets nuked by diskcheck.
If that fails and you positively don't care of what is in there, make an ubuntu live cd, boot from it, chose to not install it on the machine, after it loaded everything navigate to the drive with the folders, delete the folders.
If you don't like linux you can grab a partition tool like EaseUS partition master home, then you can resize the hdd's only partition
down to minimum possible, then you create a new partition in the unallocated space, then from My Computer you copy all the data to the new partition (leaving the nested folders there), then you delete the old partition and enlarge the new partition to fill all unallocated space.