A comprehensive infrared microscopic study of single tracks of atmospheric pressure plasma polymerised HMDSO is presented. The effects of different process parameters, i.e. the process gas, the nozzle setting (distance between discharge chamber and injection point of the monomer gas), and the nozzle speed, are investigated. It is shown that the chemical structure of singles tracks is not homogenous along the deposit. An increase of the oxygen content in the process gas or an increase of the excitation energy transferred to the monomer gas increase the relative content of SiOCH3 and SiOH units within the bulk polymer network. The deposition of superposed tracks is studied as well and it is revealed that the structure of the coating is changed compared to the first track.