Missing folders after OS X El Capitan upgrade
'All My Files" is just a Smart folder (&amp; frankly, imho, a useless one ;-)

Your files should be right where you left them in the hierarchy - right click one &amp; 'Show in Enclosing Folder' to see where it really is.

The default behaviour is that new Finder windows show "All My Files" But you can easily change this to open anywhere you like.
Go to Finder, press  Cmd ⌘   ,  (or Finder menu > Preferences… )
Select General &amp; then choose your preferred initial location from the drop menu