Surface morphologies of thin films of polypyrrole doped with two similar anions (with different ionic radii) viz. chloride and bromide were compared by means of fractal geometry. Scanning electron micrographs of the polymer surfaces showed a significant difference between the surface structures of two anion-doped polypyrrole films in microscale and particularly in nanoscale. Surprisingly, the bromide-doped polypyrrole had nanostructure; whereas, the chloride-doped polypyrrole surface was smooth in nanoscale. An electrochemical method based on gold-masking approach was employed to reveal the fractality of these polymer surfaces in microscale. Fractal geometry successfully discovered the effect of anion doping on microstructure of the conductive polymer by suggesting different fractal dimensions. In addition, SAXS analysis indicated significant difference in fractality of the polymer in nanoscale.