This one was actually easier than I thought. Robocopy seems to do a good job at this. I created a folder structure that had empty folders and some NTFS permissions. I called this folder that I wanted to copy Copytest. I then executed this Robocopy command to make a copy of this folder structure on another hard drive.
Robocopy e:\CopyTest c:\CopyTest /sec /mir
The /SEC preserves the permissions and the /MIR creates a mirror of the original location on the destination.