We have designed a system engineered to mimic biological spatial order. The system consists of nanoscale dots organized into hierarchical arrays in which structural parameters. such as spacing and orientation, are systematically varied. These arrays are used to probe the spatial distributions of binding sites in biomolecules. In this paper, we describe the fabrication process, including lithography and biofunctionalization, and we discuss issues related to surface chemistry that are critical to creating robust, biologically active nanoarrays. (c) 2005 American Vacuum Society.