This paper presents an extended, stochastic reconstruction method for catalyst layers (CLs) of Proton Exchange Membrane Fuel Cells (PEMFCs). The focus is placed on the reconstruction of customized, low platinum (Pt) loading CLs where the microstructure of CLs can substantially influence the performance. The sphere-based simulated annealing (SSA) method is extended to generate the CL microstructures with specified and controllable structural properties for agglomerates, ionomer, and Pt catalysts. In the present method, the agglomerate structures are controlled by employing a trial two-point correlation function used in the simulated annealing process. An off-set method is proposed to generate more realistic ionomer structures. The variations of ionomer structures at different humidity conditions are considered to mimic the swelling effects. A method to control Pt loading, distribution, and utilization is presented. The extension of the method to consider heterogeneity in structural properties, which can be found in manufactured CL samples, is presented. Various reconstructed CLs are generated to demonstrate the capability of the proposed method. Proton transport properties of the reconstructed CLs are calculated and validated with experimental data. (C) 2016 Elsevier B.V. All rights reserved.