Smart folders in OS X allow you to group files and folders by a number of different criteria, including name, type, size, content, and hundreds of similar attributes that are stored in the files’ metadata tags. This feature can be exceptionally convenient; however, there might be times when your smart folders do not work properly, and may show incorrect files, show only a small subset of files, or not show any files at all.

If this happens, then you may also see smart folders in various applications like iPhoto, Mail, and other applications that use file metadata stop working properly.

The overall reason for this is because of damage to your Mac’s metadata database that is used for a number of search and file information services in OS X, including not only Spotlight, but also the Finder’s “About This Mac” window that calculates storage availability, and various Smart folders.

To fix this issue, you simply need to rebuild your Mac’s Spotlight index, but before doing so, since this index has to do with details about files and folders on your Mac, you will need to be sure your drives’ filesystems are healthy and can be re-indexed without any problems.

Step One: Repair drive formatting

1. Be sure all USB, FireWire, or Thunderbolt drives on your Mac are attached and mounted.
2. Open Disk Utility, where you will see the drives in the left-hand device list.
3. Hold the Command key and then click each drive to select it. Be sure to do so for both the volumes on the drive, and the drive itself (the item above any listed volumes).
4. Go to the First Aid tab that appears, and then click the “Verify Disk” button

If any problems show when you do this, then use Disk Utility’s “Repair Disk” button to fix the drive. Note that to do this on your boot drive will require you restart to Recovery Mode and then use Disk Utility there.

Step Two: Repair boot drive permissions

1. Use Disk Utility (either in Recovery Mode or when booted normally) to select your boot volume.
2. Click “Repair Permissions” in the First Aid tab.
3. Wait for the routine to complete (there is no need to repeat this more than once).

Step Three: Disable ownership on external volumes

1. Select an external drive in the Finder and press Command-i to get info.
2. Click the lock at the bottom of the info window to authenticate.
3. Ensure the checkbox for ignoring ownership on the specified volume is checked.

Note that this step is somewhat optional, but will ensure that no odd permissions settings for files on the external drive will interfere with the metadata index rebuild.

Step Four: Rebuild your metadata index

1. Open the Spotlight system preferences pane.
2. Click the “Privacy” tab.
3. Drag all of your mounted hard drives (internal, and external) from the Finder to the Privacy list (or click the plus button to add them).
4. Remove the drives from this list once they are added.

This last step will force OS X to rebuild the metadata index on the drives, and with ensured healthy partitioning and filesystem formatting on the drive, as well as proper permissions setup on your boot drive.

Keep in mind that since Smart Folders and other metadata-handling routines in OS X depend on this database, when you have cleared it, the smart folders will not work at all. Only after the metadata index is fully rebuilt will these smart folders work properly again. During the rebuild, you may see them begin to populate with relevant files and folders as their metadata content is indexed, so the accuracy and completeness of any Smart searches you have will get better as the index is built.

If you want to check the progress of the rebuild, you should be able to do so from the Spotlight menu, where upon clicking it you will see a progress bar that at least suggests the rebuild is taking place (sometimes this does not show progress, but only a striped indication that rebuild activity is ongoing). For some reason, OS X will not always display the progress bar, so if it is not showing, then try entering a few characters in the search bar and then deleting them to see if this will spur it to show.

An alternative method of checking the indexing status is to open the Activity Monitor utility, and then sort the processes in the CPU tab by “%CPU” column, where you will see the “mds” and “mdworker” processes working to index the drive.