In addition, the PS3’s Safe Mode* feature includes options that can help with memory fragmentation.
Restore File System. Attempts to repair all areas on the hard disk drive where files can be saved. Corrupted data may be erased, which can help performance.
If you choose not to enter Safe Mode, you can manually delete corrupted saves within the XMB menu. Go to Games>Saved Game Utility. Within the menu, delete any corrupted save files. These files can be created from Skyrim and other games when a game doesn’t save properly (shutting down the console before an autosave completes, etc).
Rebuild Database. Will help with memory fragmentation on the PS3 HDD. Note: Using Rebuild Database will erase messages, playlists, changes made on [Information] screens, trimming information for pictures in [Photo], video thumbnails, video playback history and video resume information. The content that is erased will not be recoverable.
*Sony does not recommend using the options in Safe Mode unless you are experiencing issues with the PlayStation 3. Some of these options could result in loss of data.