Other than icacls provided by KCotreau answer in here, you can also handle security descriptors through PowerShell. You may want to start here:
TechNeth: Windows PowerShell Tip of the Week: Working with Security Descriptors
Take particular notice that you can set your a desirable security descriptor on one file and then use that as a template for every other file. The following commands does this:
C:\>$MyNewACL = get-acl templatefile.txt
C:\>get-childitem x:\somefolder -recurse -force | set-acl -aclobject $MyNewACL
The first command will copy the security descriptions of the file templatefile.txt, that you first set as having the settings you want to repopulate some folder with. The second command does the actual changes to all the files in that folder inside drive X (-recurse will get files and directories inside that folder, and -force will get hidden files).
See also: Set-Acl command