If your “All My Files” folder does not show any Merlin project files, and you are already using the latest Merlin update,  this is how to invoke re-indexing by Spotlight.

– From the Apple menu, choose System Preferences.
– Click Spotlight.
– Click the Privacy tab.
– Drag your home folder or even an entire volume (your hard drive) to the list.
– Remove the item or volume you just added.

Or for the Terminal geeks:
sudo mdutil -E /

Source: http://support.apple.com/kb/ht2409

If you allow the system to reindex your files for a while, Merlin project files will appear in the “Documents” area.