We have developed a multistep route to the fabrication of virus assembled nanostructures with chemoselective protein-to-surface linkers synthesized by an efficient solid-phase method. These linkers were used to create patterns of 30-to-50-nm-width-lines by scanning probe nanolithography. Genetically modified cow pea mosaic virus with unique cysteine residues at specific locations on their capsomers were assembled through covalent linkage on these patterns. The morphology of the assembled structures on these line patterns characterized by atomic force microscopy was found to be strongly influenced by the intervirion interactions.