Electrodes modified by polythiophenes bearing different substituents have been prepared and the behaviour of the conducting polymers has been studied with respect to the structural phenomena occurring in the correspondence to the doping and the relevant undoping processes. The effects of experimental parameters, such as undoping potential and time, have been investigated. The steric hindrance of the substituents on the polymer chain is demonstrated to play a fundamental role in determining the extent of compactness of the film, as induced by polarisation of the electrode at potentials at which the previously charged polymer is neutralised. Such a conclusion is in accordance with prediction of the electrochemical stimulated conformational relaxation model. Electrochemical AFM measurements have been performed in order to acquire a direct view of the morphological modifications of the polymer coatings during the reduction.