Abstract. Detailed investigation of the morphology of the pore space in clay is a key factor in understanding the sealing capacity, coupled flows, capillary processes and associated deformation present in mudstones. Actually, the combination of ion milling tools (FIB and BIB), cryogenic techniques and SEM imaging offers a new alternative to study in-situ elusive microstructures in wet geomaterials and has the high potential to make a step change in our understanding of how fluids occur in pore space. By using this range of techniques, it is possible to quantify porosity, stabilize in-situ fluids in pore space, preserve the natural structures at nm-scale, produce high quality polished cross-sections for high resolution SEM imaging and reconstruct accurately microstructure networks in 3D by serial cross sectioning.