Information about the surface topography is very important to achieve the correct elemental concentrations from the 2D X-ray intensity maps in micro-PIXE. Previously, an innovative approach of stereo-PIXE has been introduced to reconstruct the surface topography using two X-ray spectrometers in the lateral direction of the detector positions. Here, we developed the stereo-PIXE method to the four-segment Silicon drift detector (SDD), mounted at the Jožef Stefan Institute (JSI) microprobe, by considering a set of stereovision maps acquired by orthogonal segments to reconstruct the surface topography both in the lateral and longitudinal directions of the scanned area. To this aim, X-ray intensity disparity from the opposing segments was simulated for an ideal flat inclined model of the sample to infer the inclination angle across the opposing segments. Then, the obtained two gradient components of the surface topography from the inclination angles, along the axes that connect the two opposing segments, were reoriented along the scanned area with a proper rotation angle. Thus, to reconstruct the 3-D sample surface topography profile, the integration of the surface topography gradient was numerically performed in the two dimensions along the sample surface. The feasibility of the method is demonstrated on the pure Ti sample with scratched structures.