Nanopatterned arrays of biomolecules are a powerful tool to address fundamental issues in many areas of biology. DNA nanoarrays, in particular, are of interest in the study of DNA–protein interactions and for biodiagnostic investigations. In this context, achieving a highly specific nanoscale assembly of oligonucleotides at surfaces is critical. In this chapter, we describe a method to control the immobilization of DNA on nanopatterned surfaces; the nanofabrication and the bio-functionalization involved in the process will be discussed.