The control system for the Multipurpose Multiple Telescope Testbed (MMTT) is described. The phased array consists of four 20 cm telescopes, and has a 30 arcminute field of view. The maintenance of lateral pupil geometry to within one micron of the ideal is the key feature of the control system. Two mirrors behind each afocal telescope combine four beams into one, and are actuated to control both tilt and piston. Together the two beam combiner mirrors control lateral pupil geometry. The optical sensor system slowly scans the telescope field of view while monitoring the piston error verses field angle. A discrete-time-varying Kalman filter then processes these measurements to estimate lateral pupil geometry errors. The controller integrates the Kalman filter estimates, along with the x and y tilt measurements which are treated deterministically. Multiplication by an axis separator matrix converts the control input commands into appropriate piezoelectric transducer actuator commands. The entire control algorithm is implemented on a high speed array processor board. Preliminary test results show that the control system is accurately controlling lateral pupil geometry for small field angles. For larger field angles, the system was unstable due to erroneous tilt error measurements. The source of this error is discussed and a solution is proposed.