In recent years, the technical capabilities of high-resolution Scanning Electron Microscopes (SEM) improved significantly. To fully utilise their potential, it is crucial that also the preparation techniques are advanced to obtain a high-quality surface which preserves even nanometre sized microstructural features. In this study, state-of-the-art resin-embedded polishing, and novel Broad Ion Beam (BIB) milling of hydrated cement paste are compared. SEM microstructural investigations are aided by image processing to determine porosity and pore geometry factors. Additionally, a comprehensive quantitative surface roughness analysis based on Atomic Force Microscopy scans is carried out. BIB-milling enabled the study of nanoscale features such as gel porosity or the acicular morphology of calcium-silicate-hydrates. Pores exhibit increased aspect ratios whereas resin-embedded polishing results in higher circularity. However, a superior vertical surface roughness was achieved by the resin-embedded polishing approach. The research highlights the advantages and drawbacks of BIB-milling as a polishing method for hydrated cement pastes.