An encoder interferometry system includes an interferometer positioned to receive first and second beams having different frequencies, in which the interferometer has at least one polarizing beam splitting element for directing the first beam along a measurement path to define a measurement beam and the second beam along a reference path to define a reference beam. The encoder interferometry system further includes a encoder scale positioned to diffract the measurement beam at least once, a detector positioned to receive the measurement and reference beams after the measurement beam diffracts from the encoder scale, and an output component positioned to receive the measurement and reference beams before they reach the detector and deflect spurious portions of the first and second beam away from the detector.