Invisible files (etc, var, tmp) become visible after Disc Utility Restore

After cloning my hard disc to an external drive using the Disc Utility Restore function the three files var, etc, tmp have become 'visible' as aliases. How do I restore them to their 'invisible' status and how do I prevent this happening again?
The 'restored' external drive works fine as a startup disc with all other files as they should be.

Personally I think the easiest solution is to just do what all versions of OS X did up to Tiger: create the .hidden file and list the files. While Tiger no longer creates the file, the Finder will still read one if it is present. What I did was open TextEdit, set format to plain text, listed:
var
etc
tmp
Saved as hidden to the root level of the drive, then opened Terminal, did cd to /, then
mv hidden .hidden
Relaunch Finder and files are now hidden from view, without any monkeying with the files themselves. The Apple recommendation for the problem makes me feel faint.
Francine
Francine
Schwieder

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