Synthetic TAT peptides designed to contain an arginine rich basic unit can bind to RNA with an affinity and specificity of a full-length TAT protein. Therefore, deducing strategies to immobilize such short peptides to surfaces can enable one to study their unique recognition properties in various types of sensor platforms. In this paper, we present a strategy to immobilize a 15-residue TAT peptide (CGISYGRKKRRQRRR) in the form of nanoscopic features on SiOx surfaces. The protocol is based on dip-pen nanolithography that results in the formation of a covalent attachment of the peptide to a SiOx surface rather than immobilization via electrostatic interactions or patterning on metal surfaces. The nanolithography was characterized by atomic force microscopy (AFM) and X-ray photoelectron spectroscopy. Critical parameters identified by this report include roughness quality and chemical composition of the surface prior to patterning, high humidity conditions, and concentration of ink solution needed to modify the AFM tip. Furthermore, the nanoscopic features were successfully used in recognition experiments where an RNA sequence with a loop structure, known for its specific interaction with the peptide, was tested. The results in this report indicate that one can use nanolithographic strategies to pattern chemically modified "soft" SiOx surfaces and therefore provide a proof-of-concept experiment that can be transferred in complex microfabricated semiconductor architectures. Developing such patterning methodologies, along with the reported surface characterization protocol, is essential for precise and selective multicomponent placement of biologically active molecules on microcantilever based devices or other types of bio-MEMS platforms.