Dual focused ion beam-scanning electron microscopy (FIB-SEM) is frequently being used to characterize nano-scale pore structures observed in carbonate and shale gas rocks. However, applications are limited to qualitative analysis of nanopore structures. Herein, the concept of statistical representative elementary volumes (SREV) is applied to FIB-SEM data of a Cretaceous chalk sample. Lattice-Boltzmann (LB) simulations with multiple relaxation time and topological analysis show that the size of the SREV for this chalk sample can be established at ~ 10 microns based on anisotropic permeability, tortuosity, and specific surface area. This work confirms that the FIB-SEM technique can be used for the quantitative analysis of nanopore structures and highlights nano-scale basis for strong anisotropy in the presence of fractures. In addition, nanopores and pore throats are not resolved at voxel dimensions less than ~ 80 nm, resulting in significant underestimation of surface area and permeability.