Methods and systems for calibrating the location of x-ray beam incidence onto a specimen in an x-ray scatterometry metrology system are described herein. The precise location of incidence of the illumination beam on the surface of the wafer is determined based on occlusion of the illumination beam by two or more occlusion elements. The center of the illumination beam is determined based on measured values of transmitted flux and a model of the interaction of the beam with each occlusion element. The position of the axis of rotation orienting a wafer over a range of angles of incidence is adjusted to align with the surface of wafer and intersect the illumination beam at the measurement location. A precise offset value between the normal angle of incidence of the illumination beam relative to the wafer surface and the zero angle of incidence as measured by the specimen positioning system is determined.