Free-standing films of polypyrrole have been electrochemically synthesized from solutions of pyrrole and p-toluene sulphonate in water. The resulting polymer was exposed to a variety of electron-beam conditions in an analytical scanning transmission electron microscope and the interaction between the electron beam and the sample was investigated by elemental X-ray spectroscopy and electron diffraction. In transmission mode, with an 80 kV beam, the films were found to be stable with respect to the production of sulphur X-rays for up to 500 live seconds. Molecular ordering was observed to be destroyed by the action of the beam. Such techniques, together with X-ray scattering, were subsequently utilized to examine spatial variations in molecular trajectory and counter-ion content; these variations were found to be associated with the nodular surface structure that characterizes polypyrrole.