Although the physical structure and electrochemical properties of thin conducting polymer films are known to be influenced by the method used to deposit them, our understanding of where these structural differences occur and whether or not they can be removed is still uncertain. We therefore propose to examine these effects in polypyrrole films. In a first instance, the aim will be to compare films prepared using different deposition protocols which will address the effect of continuous growth as opposed to a step-by-step method for each control function (potentiodynamic, potentiostatic and galvanostatic). The second part of this study aims to determine how prolonged redox cycling and maintaining the films in a fixed charge state can affect the internal structure of the films and ultimately to establish whether or not a common structure can be achieved despite different growth protocols.