A direct-writing technique that allows the fabrication of 3D chemically active nanostructures by combining low-pressure plasma polymerization with an electron-beam process is reported. The figure shows functional nanopillars consisting of acrylic acid (carboxylic acid moieties) on a protein-repellent layer of poly(ethylene glycol). The versatility of the structuring process makes it a promising tool for probing biological systems at the nanoscale.