A beam alignment signal processing system wherein a true beam position error signal is generated regardless of beam intensity. This beam position error signal is used within a beam alignment system that maintains a desired alignment between first and second beams traveling in parallel along a desired optical path. A detector senses the position of the beams as the beams (or portions of the beams) are directed onto a surface thereof. The detector generates a set of position signals that indicate the position at which a beam, or at which an energy centroid associated with a plurality of beams, falls upon the detector surface. A first set of position signals is generated corresponding to the position of the first beam on the detector surface with the second beam turned off. These signals are stored in signal storage means. The second beam is turned back on, and a second set of position signals is generated corresponding to the position of the centroid of the first and second beams on the detector surface. A third set of position signals is then generated from the first and second set of position signals corresponding to the position of the second beam on the detector surface. The position error signal is finally generated from the first and third sets of position signals. Detector offset correction means are employed to remove the effects of detector offset from the sets of position signals. Normalization means are likewise employed to remove the effects of beam intensity variations from the sets of position signals.