In this thesis, the impact of incorporating high resolution structural features into the thermal modeling of the polymer electrolyte membrane (PEM) fuel cell gas diffusion layer (GDL) and microporous layer (MPL) is studied. Atomic force microscopy (AFM) has been used to image the surfaces of untreated Toray GDL fibres, and the nano-sized particles within Sigracet MPL. The validity of the GDL smooth fibre assumption commonly employed in literature is studied using a thermal resistance network approach. The MPL, which has been found to show structural variability between manufacturers, was also analyzed using AFM to obtain distributions for the particle size and filling radius. The equivalent thermal resistance between MPL particles was computed using the Gauss-Seidel iterative method, and was found to be sensitive to the particle separation distance and filling radius. Finally, unit-cell analysis is presented as a methodology for incorporating MPL nano-features into modeling of the MPL bulk regions.