Disclosed is a system and method for aligning a free-space optical signal in an optical system having a light modulator having an array of pixels. In this system and method, certain pixels of the light modulator array are initially assigned for the modulation of the free-space optical signal. An alignment optical signal is generated and monitored, to determine whether the optical system components are properly aligned. The alignment optical signal is generated and propagated along a path that is substantially aligned with the path of the free-space optical signal. Detector elements are used to monitor the position (and shifts in the position) of the free-space optical signal. By reassigning the pixels of the array of the light modulator at the direction of a control system, it is possible for the light modulator to compensate for shifts in the alignment of the optical components within the system.