AOTF controller that monitors output power of a plurality of wavelengths of an AOTF and scans the frequency of corresponding RF input signals to an AOTF acoustic transducer and searches for the RF frequency corresponding to each desired wavelength that provides maximum optical output for each wavelength. The controller includes a plurality of sensor inputs for monitoring the power of each wavelength output from the AOTF, and alternatively, also monitors other AOTF parameters such as temperature and/or reads AOTF identification performance data that can be stored in a EPROM on a AOTF housing. The controller includes facility for input of modulation data, and in response to the data modulates the corresponding wavelength parameter such as power. A USB bus is provided for input of programming to the controller, and for output of performance data from the controller.