Research on shale using focused ion beam/scanning electron microscopy (FIB/SEM) technology has become commercially important. However, the traditional method used in the industry tends to misinterpret reservoir properties. With the improved method discussed in this paper, results are free of perspective distortion and shading effects, and it is possible to preserve the true pore throat shape and three-dimensional (3D) volume information. Accurate pore throat information assures the most reliable calculation of porosity and permeability and benefits the prediction of shale gas/oil recovery. Furthermore, this work is not limited to shale gas/oil studies—other tight gas systems can also be investigated using this method. The same technology can also be applied to coal beds to study cleats' patterns and impurities (clays and sulfides) in coal samples.