The aim of this work was to investigate the influence of the substrate material on the plasma enhanced chemical vapour deposition and the plasma sputtering of thin films in low pressure (3-20 Pa) parallel-plate radio frequency (rf) discharges. It was observed that the deposition or sputtering rates differed above different materials, e. g. above a substrate and substrate electrode. Moreover, the substrates placed on the bottom rf electrode seemed to be mirrored in the thickness of a thin film deposited or sputtered on the upper grounded electrode. The influence of the substrate material on the plasma parameters was studied via particle in cell/Monte Carlo computer simulation. According to our finding the mirroring of the substrate was caused by different secondary electron emission yields of the substrate material and material of the substrate electrode. This difference in the secondary electron yield affected plasma density above the substrate leading to higher or lower deposition or sputtering rates on the grounded electrode. Therefore, the role of secondary electrons in the discharge was studied. Spatial distributions of impact positions on the grounded electrode for electrons and ions emitted from the rf electrode and created in the ionization avalanche of the secondary electrons were calculated in order to simulate the mirroring of the substrates.