Geological formations, such as shales and mudstones, are highly compact and challenging to characterize experimentally. Beyond artifacts associated with the chemical composition of the material, certain formations exhibit topological and morphological properties that, during each FIB ablation, generate shading effects (back-pore artifacts). As in the present case, these artifacts may prevent access to a connected pore network during reconstruction and FIB-SEM processing. This issue compounds other challenges that constrain the ability to accurately reconstruct a digital twin of the porous medium of interest. In this study, we present the solutions we have developed to mitigate common artifacts, with a particular focus on addressing back-pore artifacts. This effort aims to advance Digital Rock Physics techniques, extending their analytical capabilities for complex porous media. The workflow outlined here details the processes required to characterize mineralogy and quantify flow properties based on a representative pore-space geometry. At the Focused Ion Beam - Scanning Electron Microscopy (FIB-SEM) scale (nm to μm), characteristic of tight formations, the proposed methodology can be extrapolated to larger volumes. It enables the quantification of transport properties at the pore scale with a high degree of confidence as a function of fluid pressure. The proposed imaging process, in conjunction with the Lattice Boltzmann Method, provides an effective approach for evaluating transport properties within a given pore-scale geometry. Furthermore, it highlights the method's potential for investigating transport behavior as a function of pressure and temperature.