Production of polythiophene (PTH) and polypyrrole (PPY) thin films via double discharge plasma system has been studied. The double discharge system is a superposition of an ordinary low-pressure dc glow discharge and a high-current pulsed one. The glass substrates were located simultaneously at three different positions in the reactor and the thin films were synthesized at constant plasma parameters to evaluate the influence of the position on the molecular structure. And, the as-grown and iodine doped thin films were investigated to find out the correlation between molecular structure variation of the iodine-film interactions, too. The PTH (C4H4S) and PPY (C4H5N) monomers without using any carrier gases have been used as plasma precursors, each at 1 mbar operating pressure. The thin films were compared by using Fourier transform infrared (FTIR), X-ray photoelectron (XPS), and UV-visible absorption spectroscopy. It is found that the thin films obtained at the pulsed plasma region where the gas phase polymerization is dominated resemble to conventional polymeric structure. The XPS depth profiles revealed that while the stoichiometry of the monomer was almost preserved with the successive depth of PTH samples, but at the PPY one was not preserved. Moreover, the atomic concentration of oxygen and nitrogen observed at the surface of the films significantly drops down beneath the surface which indicates that they could be employed as anti-corrosive materials. It is found that chemical bonding with iodine take place after doping and the value of the optical band gap of polymers (E-g) are reduced proportionally with doping time. (C) 2009 Elsevier B.V. All rights reserved.