Nanopatterning of self-assembled monolayers (SAM) by electron beam lithography (EB) was developed to produce organic templates for various nanofabrication processes. EB lithography of SAMs provide a method of patterning substrates with proteins with ultrahigh resolution down to sub-10 nm on the scale of single molecule. Green fluorescent proteins (GFP), which is a spontaneous fluorescence protein isolated from the Pacific Jellyfish was chosen as a model protein. A cysteine residue at the c-terminal end of the protein by site-directed mutagenesis for the site specific modification of protein with biotin was introduced. Field-emission scanning electron microscopy was employed to observe nanostructures composed of two different types of organosilane layers. EB lithography of fluorinated SAM as an ideal template enables the high-resolution patterning of proteins with a high signal-to-noise ratio and integration of bioactive proteins into biosensors.