Surfaces with micro- and nanometer-scale patterns have many potential applications, particularly in lifescience. This article reports on a versatile, straightforward, and inexpensive approach for the creation of chemical patterns using fabricated binary colloid crystals, consisting of small and large particles, as masks for the deposition of an amino-functionalised ultrathin film by plasma polymerization. After removal of the binary colloidal mask, the characterization techniques [scanning electron microscopy (SEM) and atomic force microscopy (AFM)] reveal a surface contrast that depicts an ability of the small particles to allow diffusion of the plasma to the substrate. A plasma-polymer film is created under the small particles and the region of substrate in direct contact with the large particle remains uncoated. Numerous types of patterns and feature heights can be produced with good fidelity over areas of several cm2 by appropriate tuning of the binary colloid crystal mask morphology and the plasma-polymer deposition time. Finally, the amine groups of the patterned surface are used for covalent grafting poly(ethylene glycol) propionaldehyde (PEG-PALD) by reductive amination under conditions of reduced solubility to produce a patterned surface for directed adsorption of protein. AFM investigations show that the proteins are preferentially attached to the nanometer-scale regions of the pattern without PEG-PALD.