The smaller the features on the stamp the more important are the interactions between stamp and polymer layer. A stamp rich in small structures will effectively show a surface area enlargement, which generally leads to adhesion of the polymer to the stamp. This makes a subsequent imprint impossible without troublesome and time-consuming cleaning. The anti-adhesion properties of Si- or SiO2-based stamps can be improved by binding fluorinated silanes covalently to the surface. In this paper, we demonstrate that the deposition procedure as well as the environment during deposition are important with respect to the quality and performance of the molecular layer.