Fast indentation by atomic force microscopy allows the study of structural and physico‐mechanical properties of polymer surfaces. However, the applied load and the choice of the contact point affect the measured surface properties of the inhomogeneous material. The method of tracing the evolution of the surface structure under the load is presented. The stages of loading (tip‐surface contact, penetration into the outer surface layer revealing the internal structure) and unloading (viscoelastic recovery of the surface) are studied. Three polymers (epoxy, polyethylene, and filled rubber), whose internal heterogeneous structure is covered by a soft layer, have been analyzed. The importance of accurate determination of the contact point and the related limitations of static contact models at shallow indentation depths are shown. A dynamic model of nonequilibrium tip‐surface interaction is used to determine the surface energy and elastic modulus of the upper surface layer. The elastic moduli obtained at shallow and deep indentation depths allowed the estimation of the thickness of the layer covering the subsurface structures of the epoxy and the polyethylene. Analysis of the evolution of the filled rubber surface under the load showed the filler distribution in the matrix.