An encoder and method, such as for use in CD-ROM pre-mastering software, optimizes storage on a computer readable recording medium by eliminating redundant storage of identical data streams for duplicate files. The encoder and method detect whether two files have equivalent data streams, and encodes such duplicate files as a single data stream referenced by the respective directory entries of the files. In the illustrated embodiment, the encoder and method detect duplicate files based on file size and a cyclic redundancy check calculated on the file's data stream or portion thereof.