Microbial Fuel Cells (MFCs) are a sustainable energy technology with minimal carbon footprint, which is promising for wastewater remediation and generation of useful amounts of electricity. This study focuses on the architecture and rapid prototyping materials used for building MFCs and their effect on overall performance. Three MFC variants of the same design were constructed using ABS, PC-ISO and RC25 materials and were compared with an established MFC design. MFCs were assessed in terms of power production and COD reduction both individually and when connected electrically in parallel. In all cases the new design showed a better power output and COD removal. The order of performance in terms of power production and COD reduction for individual MFCs was PC-ISO, RC25 and ABS. However when triplets of the same materials were joined electrically together, then the order was different with RC25 outperforming ABS and PC-ISO, which was dependent on the materials' properties. It is concluded that the best performing individual MFC may not necessarily result in the best performing stack. Copyright (C) 2015, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.