Like any computer device, your PlayStation 3's hard drive can occasionally develop corrupted areas. Your PS3 will run a check for and correct corrupted data automatically if it shuts down improperly and is restarted. You can, however, initiate a correction cycle yourself using the PS3's Safe Mode, a diagnostic mode designed to correct issues that can't be addressed from within the system menu.
Entering Safe Mode
To enter the PS3's Safe Mode, start by pressing and holding the power button until the PS3 shuts down. Press and hold the power button again for about 10 seconds, at which point you'll hear a series of three beeps. After the third beep, let go of the button and then repeat the process; this time the third beep will be a double beep, at which point releasing the button will start up the PS3 in Safe Mode. You'll have to connect a controller to the PS3 via the USB cable to navigate the menu.
Restoring the File System
The "Restore File System" option in the Safe Mode menu is the tool for scanning and repairing corrupted data. This option scans all areas of the drive not allocated for firmware storage. When you select this option, it may take a few minutes to complete. Any corrupted data that can't be repaired will be deleted, meaning using this option may remove some of your data, although this data is unusable anyway.
Factory Resetting Your PS3
The "Restore PS3 System" option is the Safe Mode menu's factory reset option. Selecting this option will delete all data and settings from the hard drive, as it will reformat all data and restore the hard drive to its factory default settings. This option can also be selected from the PS3's system menu, where it performs the same task. This option will eliminate all corrupted data, but is the most extreme option available considering the loss of your data.
Preventing Hard Drive Corruption
Hard drive corruption generally occurs when a data writing procedure doesn't complete correctly, or the addition or operation of some software damages the data. Incomplete saves, wherein you turn off the PS3 before a save operation or file transfer can be completed, are a common cause of data corruption. Installing custom firmware may also corrupt some data, especially if it is done incorrectly.