Recognition of small organic molecules and large biomolecules such as proteins is of great importance in pharmaceutical as well as biological applications. Recognition inside a nanoporous membrane is particularly attractive, because of the advantages associated with ligand-receptor interactions in confined spaces. Classical nanoporous membrane-based separations simply use the difference in size of the analytes relative to pore size in the membrane. In order to bring about selectivity beyond size, it is necessary that methods for functionalizing the membrane pores are readily available. Here, we describe a simple approach to functionalize the nanopores within these membranes using self-assembling and non-self-assembling polymers. We show that these modified membranes separate small molecules based on size, charge and hydrophobicity. We also demonstrate here that proteins can be differentially transported through the nanopores based on their size and/or electrostatics.