The macroscopic properties of materials are strongly determined by their micro structure. Here, transport properties of gas diffusion layers (GDL) for fuel cells are considered. In order to simulate flow and thermal properties, detailed micro structural information is essential. 3D images obtained by high-resolution computed tomography using synchrotron radiation and scanning electron microscopy (SEM) combined with focused ion beam (FIB) serial slicing were used. A recent method for reconstruction of porous structures from FIB-SEM images and sophisticated morphological image transformations were applied to segment the solid structural components. The essential algorithmic steps for segmenting the different components in the tomographic data-sets are described and discussed. In this paper, two types of GDL, based on a non-woven substrate layer and a paper substrate layer were considered, respectively. More than three components are separated within the synchrotron radiation computed tomography data. That is, fiber system, polytetrafluoroethylene (PTFE) binder/impregnation, micro porous layer (MPL), inclusions within the latter, and pore space are segmented. The usage of the thus derived 3D structure data in different simulation applications can be demonstrated. Simulations of macroscopic properties such as thermal conductivity, depending on the flooding state of the GDL are possible. (C) 2017 Elsevier B.V. All rights reserved.