Atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and Fourier transform infrared reflection absorption spectroscopy (FT-IRRAS) were employed to understand the size, composition, and conformation of lithographic patterns composed of peptide molecules. GaAs surfaces were patterned by microcontact printing (mu CP) and dip-pen nanolithography (DPN) using a peptide sequence composed of 15 amino acids. The detailed surface evaluation showed that the patterns have similar chemical compositions but differ in the bonding among the molecules anchored on the GaAs substrate. Both types of patterns were crystalline-like in nature. The features created by DPN exhibited interchain hydrogen bonding, while the ones generated by mu CP displayed non-hydrogen bonding. The differences in the lithographic structures can be utilized in future biorecognition experiments that take advantage of the electronic properties of the GaAs substrate and the tunable behavior of the covalently anchored biomolecules on the surface.