A new 512 x 512 pixel phase-only spatial light modulator (SLM) has been found to deviate from being flat by several wavelengths. Also, the retardation of the SLM relative to voltage varies across the device by as much as 0.25 wavelength. The birefringence of each pixel as a function of address voltage is measured from the intensity of the SLM between crossed polarizers. To these responses are added a reference spatial phase measured by phase shifting interferometry for a single address voltage. Fits to the measured data facilitate the compensation of the SLM to a root-mean-square wave-front error of 0.06 wavelength. The application of these corrections to flatten the full aperture of the SLM sharpens the focal plane spot and reduces the distortion of computer-designed diffraction patterns.