I leave the windows folder options set to the default to not show hidden files/folders and then do this in a computer startup script:
md "%allusersprofile%\Microsoft\Windows\Start Menu\Programs\Microsoft System Center 2012 R2"
attrib +h "%allusersprofile%\Microsoft\Windows\Start Menu\Programs\Microsoft System Center 2012 R2"
icacls "%allusersprofile%\Microsoft\Windows\Start Menu\Programs\Microsoft System Center 2012 R2" /reset
icacls "%allusersprofile%\Microsoft\Windows\Start Menu\Programs\Microsoft System Center 2012 R2" /inheritance:r
This sets the current folder hidden or if not already installed, adds it and sets it hidden and then strips the security so the installer can't overwrite it.