New strategies are necessary for efficient separation, purification and enrichment in biotechnology, medicine, and food technology as well as in the chemical and petrochemical industries. For such applications novel high-performance materials made by molecular surface engineering (MSE) are required. MSE technology allows the development of a large spectrum of composite membranes and the solution of many separation problems. By the design of the separation layer at the molecular level, the selectivity can be adjusted to specific requirements. In this paper the application of MSE-modified high-value functional membranes for organophilic pervaporation was investigated. The pervaporation process is an interesting alternative to conventional processes from economical and technical points of view. The membrane performance for the separation of aromatic from aliphatic hydrocarbons as one of the most challenging processes in the chemical, especially the petrochemical industry, including selected results of an industrial pilot plant study, is shown. First results for a further application of organophilic pervaporation (desulfurization of FCC naphtha) are presented.