The development of new radiation detectors of different semiconductor materials (Si, CdTe, GaAs, …) brings the necessity to test and evaluate their response and detection performance such as the spatial homogeneity and local charge collection efficiency. A number of these materials exhibit a certain degree of inhomogeneity, which is needed to be determined in order to eliminate its negative effects. Similarly, such testing is desired as well in order to determine the extent of radiation damage in detectors. We decided to build a size-configurable beam and detector positioning system to probe the collection of charge spatially localized deposited by X-rays on a pixelated detector. The principle of this system is based on the use of a collimated parallel X-ray beam with a line profile, which delivers a defined charge at a specific location in 3D in the sensor. The beam can be sent onto the pixelated sensor at a low angle, which allows determining, for a given angle and detector position, the depth of interaction for each pixel. Shifting the detector along the axis perpendicular to the plane of the beam we can obtain a map of the detector response which is in 3D—i.e. both across the sensor plane and along its depth. Per-pixel signal read out from the pixelated detector can be done by usage of the hybrid semiconductor device Timepix which allows per-pixel energy measurement. The Timepix chip contains an array of 256×256 square pixels (total over 65 k pixels) with pitch size 55 μm. Our method allows probing and scanning the collection of charge at different depths across the pixelated sensor. Moreover, it allows determining the effect of radiation damage at μm scale. All these effects can be studied as well in the dependence on various detector parameters such as the sensor bias voltage. Results with a specific detector are presented.