Electrochemically synthesised polypyrrole (PPy) with 1,5 naphthalene disulfonate (1,5-NDS) counterions treated with simple acid and base was characterised using X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS). The as synthesised film was found to be amorphous with short-range ordering in the polymer backbone. Ordering was lost after thermal ageing with evidence of counterion degradation. Base treatment lead to loss of ordering as well as dedoping of the polymer whereas acid treatment at high temperature increases short range ordering. Conductivity was also increased dramatically with evidence of ion exchange. Ordering induced by the treatment was maintained even after thermal ageing.