The approach for ripple nanopattern construction on surface of two polymer substrates [polyethylene naphthalate (PEN) and polystyrene (PS)] exposed by a KrF pulse excimer UV laser through a contact lithographic mask with circular slit was proposed in this paper. Thin layer of gold was deposited on samples after the laser treatment. Changes in the morphology of the surface of both the shielded and exposed areas of the substrates, as well as the dimensions of the laser‐induced periodic surface structures, were determined (by atomic force microscopy, laser confocal microscopy and scanning electron microscopy), compared with observations and measurements made on samples treated directly (without a contact mask) under the same conditions. The morphology of the interface between the treated and untreated regions was also closely studied. Surface chemistry of treated samples was studied in detail by X‐ray Photoelectron Spectroscopy. The detailed study of surface chemistry of modified PEN and PS revealed a significant increase of oxygen concentration for laser treated PS and increase of carboxyl groups in case of PEN. The potential application of this research can be found in biotechnology, micro technology and several other fields. Copyright © 2016 John Wiley & Sons, Ltd.