A wafer is moved under an inspection spot by a rotary inspection system. The system rotates the wafer about an axis of rotation and translates the wafer along a linear trajectory. When the inspection spot is not aligned with the trajectory of the axis of rotation, an angular error is introduced in the representation of the position of the inspection spot with respect to the wafer by the rotary encoder. The angular error is corrected based on an angular error correction value. The angular error correction value is determined based on the distance between the inspection spot and the trajectory of the axis of rotation, the radial distance between the axis of rotation and the inspection spot at a first instance of a particular angular position, and a second radial distance between the axis of rotation and the inspection location at a second instance of the angular position.