Gas storage and flow behavior in the shale gas rocks are complex and hard to identify by conventional core analysis. This study integrates clustering analysis techniques from material science, petrophysics, and petrology to characterize North American shale gas samples from Utica, Haynesville, and Fayetteville shale gas plays. High pressure (up to 60,000 psi) mercury porosimetry analysis (MICP) determined the pore size distributions. A robust, detailed tomography procedure using a dual-beam (Scanning Electron Microscope and Focused Ion Beam, also called SEM-FIB) instrument successfully characterized the submicron-pore structures. SEM images revealed various types of porosities. Pores on a scale of nanometers were found in organic matter; they occupy 40–50% of the kerogen body. Two-hundred two-dimensional SEM images were collected and stacked to reconstruct the original pore structure in a three-dimensional model. The model provided insights into the petrophysical properties of shale gas, including pore size distribution, porosity, tortuosity, and anisotropy. This paper presents the pore model constructed from Fayetteville shale sample. The work used X-ray diffraction (XRD) to semi-quantify shale gas clay and non-clay minerals. The Haynesville and Utica (Indian Castle formation) shale samples have a high illite content. The Utica (Dolgeville formation) shale samples show high calcium carbonate (calcite) content. Moreover, wettability tests were performed on the shale samples, and the effect of various fracturing fluid additives on their wettability was tested. Most additives made the shale gas surfaces hydrophilic-like (water-wet).