A treatment pattern (such as a focused spot, an image, or an interferogram) projected on a treatment target may lose precision if the treatment beam must pass through a birefringent layer before reaching the target. In the general case, the birefringent layer splits the treatment beam into ordinary and extraordinary components, which propagate in different directions and form two patterns, displaced from each other, at the target layer. The degree of birefringence and the orientation of the optic axis, which influence the amount of displacement, often vary between workpieces or between loci on the same workpiece. This invention measures the orientation of the optic axis and uses the data to adjust the treatment beam incidence direction, the treatment beam polarization, or both to superpose the ordinary and extraordinary components into a single treatment pattern at the target, preventing the birefringent layer from causing the pattern to be blurred or doubled.