This work aims at presenting an innovative method for tailoring the morphology of functionalized plasma polymer films (PPF). The approach is based on the formation of a plasma polymer bilayer system in which the two layers differ by their chemical composition and cross-linking degree. As a case study, propanethiol-based plasma polymer films have been investigated. As revealed by a much higher S/C ratio than in the propanethiol precursor (i.e. 0.83 vs 0.33), it has been demonstrated that the bottom layer contains a large fraction of trapped sulfur-based molecules (e.g. H2S). When further covered by a denser PPF formed at higher energetic conditions, a three-dimensional morphological reorganization takes place giving rise to the micro/nano structuration of the organic material. The shape, the dimensions as well as the density of the generated structures are found to depend on the thickness of both coatings involved in the bilayer structure, offering a great flexibility for surface engineering. Annealing experiments unambiguously confirm the major role played by the sulfur-based trapped molecules for inducing the reshaping process. The whole set of data clearly paves the way for the development of an innovative approach for finely tailoring the morphology of functionalized PPF at the micro/nano scale.