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We describe FMMD controller and software for MPI system based on mechanical FFL movement. MPI based on mechanical FFL movement requires signal processing such as signal excitation, amplification, filter, and acquisition. And it is essential to synchronize the acquired signal with the mechanical FFL movement. For signal processing, FMMD controller that can adjust the attenuation and amplification factors and filtering frequencies of signals in real time was used. The signal acquired from the controller was transferred to the host PC, and the synchronization between the signal acquired from the MPI device and the mechanical FFL motion was processed, and the frequency analysis of the synchronized data was performed in software. Without using various commercial signal processing equipment, we were able to develop MPI system by using the controller and software.