Methods and systems for reducing the effect of finite source size on illumination beam spot size for Transmission, Small-Angle X-ray Scatterometry (T-SAXS) measurements are described herein. A beam shaping slit having a slender profile is located in close proximity to the specimen under measurement and does not interfere with wafer stage components over the full range of angles of beam incidence. In one embodiment, four independently actuated beam shaping slits are employed to effectively block a portion of an incoming x-ray beam and generate an output beam having a box shaped illumination cross-section. In one aspect, each of the beam shaping slits is located at a different distance from the specimen in a direction aligned with the beam axis. In another aspect, the beam shaping slits are configured to rotate about the beam axis in coordination with the orientation of the specimen.