To investigate the nanostructure of polymer electrolyte fuel cell catalyst layers, focused ion beam scanning electron microscopy (FIB-SEM) tomography is a common technique. However, as FIB-SEM tomography lacks of image contrast between the catalyst layer and its pores, state-of-the-art reconstruction methods by threshold cannot accurately distinguish between these two phases. We show that this inability leads to an underestimation of the porosity by a factor of nearly two, a reconstruction with channel-like artifacts and that these artifacts make it impossible to calculate reliable diffusivities. To overcome this problem, we fill the pores of the catalyst layer with ZnO via atomic layer deposition prior to tomography. By using atomic layer deposition, even smallest pores can be filled with ZnO, which exhibits a good contrast to the catalyst layer in SEM images. As a result, we present the porosity of the catalyst layer (65%) and its three-dimensional representation without typical reconstruction artifacts. Calculated O-2 diffusivities (23.05-25.40 x 10(-7) m(2) s(-1)) inside the catalyst layer are in good agreement with experimental values from the literature. Furthermore, filling with ZnO permits the identification of large Pt clusters inside the catalyst layer, which were estimated to reduce the catalyst surface area by 9%. (C) 2015 Elsevier B.V. All rights reserved.