Sectioning of a glassy polymer, poly(methyl methacrylate), at nanoscale was carried out by means of an ultramicrotome. The effects of sectioning thickness and speed on the morphology and stiffness over the sectioned surface were then investigated by atomic force microscopy. A critical sectioning thickness and speed were identified, below which flat and smooth surfaces were created with homogeneous elasticity. Above the critical thickness or speed, periodic localized structures formed on the sectioned surfaces, leading to a nonhomogeneous distribution of the mapped elasticity. Finite element simulation reproduced the periodic structures observed in the experiments. The influence of sectioning speed on the surface stiffness was predicted by a phenomenological damage model and was found to correlate with the experimental results. The study lends confidence that critical sectioning conditions (e.g., the sectioning thickness and speed) can be identified to avoid undesirable local deformation and damage in the manufacture of small scale optical and photonic components and devices. POLYM. ENG. SCI., 58:1849-1857, 2018. (c) 2017 Society of Plastics Engineers