Surface modification of polydimethylsiloxane (PDMS) under O2 plasma exposure is studied by XPS and real time ellipsometry. Results show the conversion of the PDMS surface into a SiOx-like material. Total layer thickness and extension of the SiOx layer are controlled by the sample bias. We suggest that surface and line edge roughness defects occurring when using PDMS as top layer in bilayer lithography are intimately related to the rapid kinetics of conversion and to the formation of SiOx hard micromasks on the surface.