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How to Set up Folder Permissions on Windows 2003 Server

We have 25 PC's and 25 Users. Computer names are: SYSTEM1, SYSTEM2, SYSTEM3, etc.
We have 25 folders set up with user names: Rick, Mary, Tom, etc.
If we remove the "parent" security properties from the folder and just add the computer name,example SYSTEM1 to folder Rick we have determined that ONLY Rick can get in.
Question. By us removing the "parent" security properties from the folder will our nightly system server backup still back up ALL the files? Our concern is that by us removing the "parent" security properties something else all the server may have been compromised.

Thanks in advance for any help
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Mohamed Osama
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jb2286

Admin3k is spot on from what I can tell.  One other thing is to check the permissions for the parent directory for any "Deny" instances.  Even with 99% allowed actions, Active Directory seeing any user or group with 1 "Deny" access will be denied, despite being mostly "allowed".