That's where MS Security Configuration & Analysis snap-in combined with
security templates are your friend.
Christopher Fisk wrote:
We had a machine recently come in where filesystem permissions were all
screwed up after removing a virus and cleaning off some spyware. We
could certainly have gone through and made sure permissions on each
folder were corrected, and that permissions on each file were corrected,
but the amount of time to do that manually far outweighed the
format/reinstall/restore data method we ultimately used.
I'd never seen anything like it prior to that though, so I kind of think
the filesystem itself was screwed up (Which spinrite didn't find any
errors on the drive, and our scandisk tools didn't either, but eh)