The morphological stability of polymer films is critically important to their application as functional materials. The deformation of polymer surfaces on the nanoscale may be significantly influenced by geometrical confinement. Herein, we constructed a mechanically heterogeneous polymer surface by phase separation in a thin polymer film and investigated the deformation behavior of its nanostructure (similar to 30 nm thickness and similar to 100 nm average diameter) with tapping-mode atomic force microscopy. By changing different scan parameters, we could induce deformation localized to the nanostructure in a controllable manner. A quantity called the deformation index is defined and shown to be correlated to energy dissipation by tip sample interaction. We clarified that the plastic deformation of a polymer on the nanoscale is energy-dependent and is related to the glass-to-rubber transition. The mobility of polymer chains beneath the tapping tip is enhanced, and in the corresponding region a rubberlike deformation with the lateral motion of the tip is performed. The method we developed can provide insight into the geometrical confinement effects on polymer behavior.