One vital component in the Proton Exchange Membrane Fuel Cells (PEMFCs) is the Gas Diffusion Layer (GDL). This layer is a pathway for the reactants to reach the reaction site and for the by-products to be removed. Due to this application, the permeability of this layer has been investigated experimentally and numerically [1]. This layer has a highly porous structure, and hence identifying a geometry that resembles best the GDL for modeling flow through this layer is very important. In this study, the 3D image of a GDL sample has been obtained with high resolution imaging, X-ray microtomography, and is used as a model to simulate flow through this layer. This layer typically treated with micro-porous layer (MPL). In this paper, MPL was separated and permeability through the MPL is investigated separately using an image-processing method developed in-house. The results indicate that MPL reduces the permeability of GDL considerably. This work facilitates the study of the effect of MPL on the permeability of the GDL, which is impossible to be determined in experimental approaches [2]. [1] J. Pharoah, "On the permeability of gas diffusion media used in PEM fuel cells," J. Power Sources, vol. 144, pp. 77-82, 2005. [2] J. Ihonen, M. Mikkola and G. Lindbergh, "Flooding of gas diffusion backing in PEFCs physical and electrochemical characterization," J. Electrochem. Soc., vol. 151, pp. A1152-A1161, 2004.