This paper demonstrates an improved method to accurately extract the surface morphology of black silicon (BSi). The method is based on an automated Xe+ plasma focused ion beam (PFIB) and scanning electron microscope (SEM) tomography technique. A comprehensive new sample preparation method is described and shown to minimize the PFIB artifacts induced by both the top surface sample-PFIB interaction and the non-uniform material density. An optimized post-image processing procedure is also described that ensures the accuracy of the reconstructed 3D surface model. The application of these new methods is demonstrated by applying them to extract the surface topography of BSi formed by reactive ion etching (RIE) consisting of 2 µm tall needles. An area of 320 µm2 is investigated with a controlled slice thickness of 10 nm. The reconstructed 3D model allows the extraction of critical roughness characteristics, such as height distribution, correlation length, and surface enhancement ratio. Furthermore, it is demonstrated that the particular surface studied contains regions in which under-etching has resulted in overhanging structures, which would not have been identified with other surface topography techniques. Such overhanging structures can be present in a broad range of BSi surfaces, including BSi surfaces formed by RIE and metal catalyst chemical etching (MCCE). Without proper measurement, the un-detected overhangs would result in the underestimation of many critical surface characteristics, such as absolute surface area, electrochemical reactivity and light-trapping.