Deep Freeze protects the computer by utilizing a separate partition on the hard disk drive for write back. When the computer is rebooted, this partition is treated empty again and existing information on it is unaccessible. This allows users to make 'virtual' changes to the system, giving them the appearance that they can modify core files or even delete them, and even make the system unusable to themselves, but upon reboot the 'frozen' state of the operating system is restored.

To make changes, a system administrator must 'unfreeze' the system partition, make any needed changes, and 'freeze' it again. These changes, in this way, are saved to the protected partition instead of the 'unfrozen' write back partition.