We present a novel approach for preparation of nanometric protein arrays, based on binding of avidin molecules to nanotemplates generated by conductive AFM lithography on robust oligo(ethylene glycol)-terminated monolayers on silicon (111) surfaces that are protein-resistant. We showed that only biotinated-BSA but not the native BSA bind to the avidin arrays and that the resulting arrays of biotinated BSA could bind avidin to form protein dots with a feature size of approximately 30 nm. This result demonstrates that the avidin array may serve as templates for preparation of nanoarrays of a wide variety of biotin-tagged proteins for studying their interactions with other protein molecules at nanoscale.