The microporous layer (MPL) in polymer electrolyte fuel cells is known to enhance performance and durability of the membrane electrode assembly. However, its key structural parameters and transport properties are difficult to determine due to the lack of MPL-specific measurement techniques. The present work aims to establish a specialized framework for 3-D image based morphological characterization of MPLs. The proposed framework features a tuned focused ion beam-scanning electron microscope (FIB-SEM) imaging technique and an in-house developed procedure for image processing and reconstruction of the true 3-D structure which is validated with measured porosimetry data for a pure MPL sample. The effects of FIB milling parameters are evaluated and tuned to prevent image bias and damage to the delicate MPL structure. The pore size distribution of the reconstructed MPL structure is determined using a novel algorithm based on 3-D Euclidian distance transform and the results are found to be in good agreement with the measured data. Three reconstructed domains containing the structural information are generated to account for directional and spatial heterogeneity of the material and utilized as numerical domains for calculation of key MPL material properties, namely effective diffusivity, tortuosity, and effective thermal conductivity. By comparing the obtained material properties in the through-plane and in-plane directions, the MPL material is determined to be isotropic.