After restoring a backup, the various OS X system folders became visible again (such as /bin /mach_kernel etc)

The following command (adapted from this post by Wowzera) will hide them again:

# Hide sym-links
SETFILECMD="/Developer/Tools/SetFile"
for cdir in /etc /tmp /var;
    do sudo $SETFILECMD -P -a V $cdir;
done
 
# Hide directories
for cdir in /bin /cores /mach_kernel /private /sbin /usr /Volumes; do
    sudo $SETFILECMD -a V $cdir;
done

Launch Terminal (in Applications, then Utilities), and paste the above script.