Atomic force microscopy (AFM) was used to fabricate well-defined peptide templates onto GaAs surfaces via Dip-Pen Nanolithography (DPN). DPN is a powerful technique to write specific organic and/or inorganic molecules onto a surface with an AFM tip. In this work, DPN was used to construct arrays of peptides with nanometer features. TAT peptides (e.g. CGISYGRKKRRQRRR) which exhibit rapid uptake in cells, were patterned onto the surface in either contact or tapping mode. Several techniques were used for the characterization of the modified surfaces: X-ray photoelectron spectroscopy (XPS), Fourier Transforms Infrared (FT-IR) spectroscopy and contact angle. Transmission FT-IR provided structural information such as peptide conformation. The complementary analysis confirmed the binding of the peptide onto the substrates and allowed to quantify the density of immobilized peptides on a given surface. 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 GaAs surfaces, and therefore provide a proof-of-concept experiment that can be transferred in complex microfabricated semiconductor architectures.