Characterization of the microstructure and pores in fine-grained geo-materials like mudstones is challenging because of their heterogeneity and small pore sizes. Combining Broad Ion Beam (BIB) polishing and Scanning Electron Microscopy (SEM) enables the visualization of microstructure and pores from millimetres down to a few nanometres in size. In the SEM, the BIB-polished section is mapped at high magnification with various detectors and the different features are segmented and quantified using image processing algorithms. This technology is applied on undeformed and naturally or experimentally deformed rock samples to analyse the strain behaviour of potential host rock formations of nuclear waste such as the Boom Clay and Callovian-Oxfordian Clay. Application of BIB-SEM in combination with Wood’s Metal Injection allowed imaging the connected pore space in fine-grained rocks like the Boom Clay and Ypresian Clay. The in-situ fluid distribution of saturated rocks can be imaged by applying BIBSEM at cryogenic conditions. These applications aim to increase understanding in deformation mechanisms, sealing capacity and transport properties of fine-grained materials.