Black silicon (bSi) is a promising surface texturing technology in the PV industry as it can provide superior optics and is compatible with a broad range of substrates. An accurate description of the bSi surface topography can help studying the impact of subsequent solar cell processing, assessing the uniformity of surface coatings, detecting non-ideal surface features when developing new techniques, and enabling the development of fast and scalable modelling tools. Typically, surface topography is studied by atomic force microscopy (AFM). However, this approach has limitations and can result in spurious data, such as resulting from a dull probe tip, or inadequate tip geometry when probing high aspect ratio features. Focused Ion Beam (FIB) - Scanning Electron Microscopy (SEM) based 3D tomography is an alternative candidate for studying surface topography and overcoming probe-related limitations. In this work, we employ modified sampling procedures to protect the microstructures. Instead of Ga+ FIB, we use the high power Xe+ Plasma FIB (PFIB) combined with SEM to iteratively cross-section the substrate and extract the true 2D profiles. We then use these profiles to reconstruct a 3D model that highly resemble to the SEM image of the specimen.