You can do this with robocopy.
Assuming a source C:\inetpub\site1 and destination of C:\inetpub\site2, the following will create an identical folder hierarchy under "site2", preserving the permissions of "site1".
robocopy C:\inetpub\site1 C:\inetpub\site2 /mir /copyall /xf */mirMirror/copyallCopy all permissions/xf *Exclude files matching *
