Low temperature atmospheric pressure plasma processes can be applied to inactivate micro-organisms on products and devices made from synthetic and natural polymers. This study shows that even a short-time exposure to Ar or Ar/O-2 plasma of an atmospheric pressure plasma jet leads to an inactivation of Bacillus atrophaeus spores with a maximum reduction of 4 orders of magnitude. However, changes in the surface properties of the plasma exposed material have to be considered, too. Therefore, polyethylene and polystyrene are used as exemplary substrate materials to investigate the effect of plasma treatment in more detail. The influence of process parameters, such as type of operating gas or jet-nozzle to substrate distance, is examined. The results show that short-time plasma treatment with Ar and Ar/O-2 affects the surface wettability due to the introduction of polar groups as proofed by X-ray photoelectron spectroscopy. Furthermore, atomic force microscopy images reveal changes in the surface topography. Thus, nanostructures of different heights are observed on the polymeric surface depending on the treatment time and type of process gas.