The Intelligent Media Storage System (12) disclosed herein protects computer programs and data files being copies and used in unauthorized manner. An Intelligent Control Element (12a) is installed between a computer system (14) and a mass storage device (10) and is disposed between a message storage device interface (12b) and a computer system interface (12c). The Intelligent Control Element (12a) is responsible for writing data to and reading data from the protected mass storage device (10) using special coding and encryption mechanisms. In one embodiment, the mass storage interfaces are partitioned into separate protected and unprotected mass storage interfaces. In other embodiment, coding and encryption by the Intelligent Control Element (12a) of data stored onto protected mass storage device (10) connected to the Intelligent Media Storage System (12) provides another level of protection.