Complex bis terthiophene porphyrin conducting polymers were used to investigate the uptake of zinc into the freebase porphyrin unit after polymerisation by acquiring depth profiles using Rutherford Backscatting Spectrometry (RBS) analysis. Issues such as the influence of the support material and extent of polymer oxidation on the dispersion of the counter ions through the polymer films are of importance. Gaining knowledge of the dispersion of counter ions provides new insights into the redox mechanisms for conductive polymers. The results were compared to those obtained from a sample where zinc was coordinated to the porphyrin prior to the polymerisation process. Unexpectedly high concentration of both nitrogen and oxygen were found which could be due to evidence of the trapped cations from the electrolyte ((Bu)4N+), and trapped water molecules, within the polymer films. The chlorine concentrations help to understand the dispersion of the perchlorate counter ion throughout the polymer films, and the combination of both RBS and Proton Induced X-ray Emission (PIXE) show that trace element impurities can be detected using ion beam analysis which other analytical techniques are unable to do.