A method for reducing duplicate data of an active file system, where the data is stored on a storage device of a storage system, is disclosed. A persistent image of the active file system is generated at a first point in time. At a later time, a sequence of steps to compare the active file system with the persistent image is initiated. Then, if a block of data of the active file system is identical to the data in the persistent image, the active file system is directed to refer to the persistent image for data of the file. Alternatively, if the block of data of the active file system is not identical to the data in the persistent image, the active file system is directed to refer to the data of the active file system. A file folding command may be issued to start the comparison.