The gas diffusion layer (GDL) is undoubtedly one of the most complicated components used in a polymer electrolyte fuel cell (PEFC) in terms of liquid and gas transport phenomena. An appropriate fuel cell design seeks a fundamental study of this tortuous porous component. Currently, porosity and gas permeability have been known as some of the key parameters affecting liquid and gas transport through the GDL. Although these are dominant parameters defining mass transport through porous layers, there are still many other factors affecting the transport phenomena and overall cell performance. In this work, the microstructural properties of Toray carbon papers with different thicknesses and for polytetrafluoroethylene (PTFE) treated and untreated cases have been studied based on scanning electron microscopy (SEM) image analysis. The water droplet contact angle, as a dominant macroscale property, along with the mean pore diameter, pore diameter distribution, and pore roundness distribution, as important microscale properties, have been studied. It was observed that the mean pore diameter of Toray carbon paper does not change with its thickness and PTFE content. Mean pore diameter for Toray carbon papers was calculated to be around , regardless of their thicknesses and PTFE content. It was also observed that the droplet contact angle on the GDL surface does not vary with the GDL thickness. The average contact angle for the 10 wt. % PTFE treated GDLs of different thicknesses was measured at about . Finally, the heterogeneous in-plane PTFE distribution on the GDL surface was observed to have no effect on the mean pore diameter of GDLs.