A transaction safe file system uses two sets of file allocation tables and bitmap images to perform file modifications on one of the sets while the other set remains a last known good set. After a modification is complete, a pointer is changed to the newly modified set, and the newly modified set becomes the last known good set. The sets are then synchronized. The file allocation table is used to define cluster chains while the bitmap image is used to determine if a cluster is free or not. In some operations, only the bitmap image may need to be manipulated. The file system may be used in a transaction safe mode as well as a non-transaction safe mode.