A new approach of selective membrane-based separation has been developed by coating molecularly imprinted nanoparticles onto the surface of a membrane disc whereby a selective composite membrane shall be realized. The imprints at the surface of the nanoparticles are comparable to footprints of specific molecules. These molecules are present during the synthesis of the particles and serve as a molecular template, thus imprinting their shape in the forming particle. The selectivity of the nanoparticles was shown in particle suspension using an enantiomeric model template. The permeability and porosity of the nanoparticle layer were determined by experiments for investigation of feasibility under hydrodynamic aspects. The Carman-Kozeny equation was modified and validated as an applicable theoretical model. The combination of a cost-efficient membrane disc as support for an selective nanoparticle layer can provide an efficient way in purification and sensing processes.