Go to DOS prompt, then change to directory containing the folder you want to delete, then delete each folder in turn.
If you delete files from the DOS prompt, Windows will not keep all the file info - that's probably the actual problem, the directory tree of each file to be deleted has to be saved, etc. and the overheads are two much for RAM, etc.
BTW, deleting a file in Windows does not free up space on your hard drive - the file is kept in the recycle bin - so the space is not actually freed up until the bin is emptied...
