Proton exchange membrane fuel cells (PEMFCs) are being developed as alternative energy sources for both residential and automotive applications. For this technology to reach its full commercial potential, however, a significant reduction in cost is still required while the performance and durability of PEMFCs being maintained or improved. The key in this process is continuous improvement of membrane electrode assembly (MEA) through both the development of new materials and the optimization of the 3D structural arrangement of individual MEA components. Structural optimization of MEA remains to be challenging due to multiple materials interacting across 6 orders of magnitude in their characteristic length scales, from several nanometers for the catalyst particle size to hundreds of micrometers for carbon fibers in porous transport layer. In recent years, several microscopy techniques have become widely available to characterize the three-dimensional (3D) structure of PEMFC catalyst layers. Due to the heterogeneous nature of the PEMFCs sample, a correlative, multi-scale imaging protocol is developed in this work. By combining 3D imaging data at multiple scales, an unified structural characterization workflow is developed.