In this study, the microporous layer (MPL) of the polymer electrolyte membrane (PEM) fuel cell was analysed at the nano-scale. Atomic force microscopy (AFM) was utilized to image the top layer of MPL particles, and a curve fitting algorithm was used to determine the particle size and filling radius distributions for SGL-10BB and SGL-10BC. The particles in SGL-10BC (approximately 60 nm in diameter) have been found to be larger than those in SGL-10BB (approximately 40 nm in diameter), highlighting structural variability between the two materials. The impact of the MPL particle interactions on the effective thermal conductivity of the bulk MPL was analysed using a discretization of the Fourier equation with the Gauss-Seidel iterative method. It was found that the particle spacing and filling radius dominates the effective thermal conductivity, a result which provides valuable insight for future MPL design. •Nano-scale characterization of MPL materials.•Atomic force microscopy used to analyse MPL particles and nano-features.•Numerical determination of thermal resistance between MPL particle structures.•Data presented for use in future stochastic MPL models.