Depth-sensing devices such as atomic force microscope have been widely used to characterize the morphology, nanostructure, surface composition and local materials properties of heterogeneous polymers. Such measurements are based upon a fundamental hypothesis that the deformation of polymer is elastic, that is, there is no tip-induced surface inelastic alteration or damage. Using molecular dynamics simulations, we show that the inelastic alteration at heterogeneous polymer surfaces induced by the sensing tip is intrinsic and unavoidable. Such tip-induced alteration arises from the differences in Van Der Waals interactions between different atomic species in the polymer and in the sensing tip, leading to atomic shuffling and re-shuffling, which cause inelastic alteration in both molecular structures and mechanical properties at and near the polymer surface. The present work highlights the need to reinterpret the data obtained from depth-sensing testing by considering this intrinsic inelastic deformation occurring at and near heterogeneous polymer surfaces. (C) 2015 Elsevier Ltd. All rights reserved.