Ultrahigh resolution patterning, preferably carried out by DIP PEN™ nanolithographic printing, can be used to construct peptide and protein nanoarrays with nanometer-level dimensions. The peptide and protein nanoarrays, for example, exhibit almost no detectable nonspecific binding of proteins to their passivated portions. This work demonstrates how DIP PEN™ nanolithographic printing can be used in a method to generate high density protein and peptide patterns, which exhibit bioactivity and virtually no non-specific adsorption. It also shows that one can use AFM-based screening procedures to study the reactivity of the features that comprise such nanoarrays. The method encompasses a wide range of protein and peptide structures including, for example, enzymes and antibodies. Features at or below 300 nm can be achieved. In a preferred embodiment, parallel printing with multipen systems are used.