A new characterisation method, based on the utilisation of focussed ion beam-scanning electron microscopy (FIB-SEM), has been employed for the evaluation of morphological parameters in porous monolithic materials. Sample FIB serial sectioning, SEM imaging and image processing techniques were used to extract the pore boundaries and reconstruct the 3D porous structure of carbon and silica-based monoliths. Since silica is a non-conducting material, a commercial silica monolith modified with activated carbon was employed instead to minimise the charge build-up during FIB sectioning. This work therefore presents a novel methodology that can be successfully employed for 3D reconstruction of porous monolithic materials which are or can be made conductive through surface or bulk modification. Furthermore, the 3D reconstructions were used for calculation of the monolith macroporosity, which was in good agreement with the porosity values obtained by mercury intrusion porosimetry (MIP).