Direct experimental study elastomer composites (rubber) at the phase boundary of the polymer filler is associated with a number of technical difficulties. The method of manufacture and experimental study of the mechanical properties of nano-layers of synthetic polyisoprene on carbonated surface using an atomic force microscope. Carbon surfaces prepared by ion beam treatment polystyrene layer on the wafer. Then, by centrifuging them synthetic polyisoprene applied layers of different thicknesses (from 5 to 45 nm). Using atomic force microscopy were obtained depending on the deviation of the indenter approaching the console and pressing a probe into the polymer layers. It is found that the strength of Van der Waals forces between the tip and the surface of the polymer increases significantly with decreasing thickness. The numerical solution of the problem of introducing the probe of an atomic force microscope in the polymer film is firmly bonded to the flat deformable substrate. It is assumed that the film material is purely elastic and mechanical properties can be described by neogukovogo potential. Comparison of experimental and calculated data show a significant increase in stiffness nanolayers carbonized near surface. This suggests that similar processes may be typical for elastomer composites filled with carbon particles (soot).