The electrochemical polymerization of 3,4-ethylenedioxythiophene (EDOT) in a polyanion, sodium poly(styrene-4-sulfonate)(NaPSS), has been performed through three different oxidative electropolymerizations on flexible electrodes. These electrodes have been fully characterized both at a macroscopic and microscopic scale. The morphology, characterized by Scanning Electron Microscope (SEM) and Atomic Force Microscope (AFM) reveals a tendency of PEDOT:PSS to arrange in cauliflower-like shape. Homogeneity, grain dimension and electrical properties of the PEDOT layers can be tuned by choosing different polymerization routes and different parameters of electropolymerization. At the macroscopic level, we achieved a significant decrease of the impedance of the whole electrode after the electropolymerization thanks to an increase of both the intrinsic conductivity and the roughness of the electrode surface. Moreover Conductive Atomic Force Microscopy (C-AFM) study shows for the first time a clear relation between surface topography and local conductivity of the deposed film and help to clarify the conduction mechanism in electrodeposited PEDOT:PSS layers. The deposition was also shown to be very stable and resistant through thermal accelerated ageing tests that can mimic the behaviour of an implanted electrode after several months at human body temperature. The long term stability coupled with the low impedance make these electrodes suitable candidates for long-term neural probe applications.