Nano-fillers in nanocomposites may grant the matrix material new exceptional properties or improve the existing ones. Usually the effect depends on how frequent the filler is distributed in the matrix. If the filler is well dispersed, then we need a smaller amount of nanoparticles to achieve the same effect. Therefore, it is important to be able to quantitatively characterize a composite, to determine the most useful concentration of nano-filler. Here we propose a new method for polyisoprene – carbon black (Pi-CB) nano-composite characterization with the electro-conducting mode of atomic force microscopy (EC-AFM). In this method electro-conductive channels (ECC) are measured with EC-AFM, and a three dimensional data set is obtained.