We have succeeded in aligning gold nanoparticles (Au NPs) in three-dimensions using tobacco mosaic virus (TMV) in order to realize new optical properties. TMV is a tube-shaped plant virus about 300 nm in length with an outer- and inner-diameter of 18 nm and 4 nm. We genetically fused material-binding peptides that can promote metal crystallization, namely a gold-binding peptide (GBP) and a titanium-binding peptide (TBP), to the outer-surface of TMV. By reducing potassium chloroaurate with sodium borohydride in the presence of the engineered viruses in 5% acetic acid solution, Au NPs were deposited on the outer-surface of the viruses. Using TBP-fused TMV, NPs of 5 nm were obtained, with a standard deviation smaller than those deposited on wild-type TMV. The diameter of the NPs on GBP-fused TMV was 10 nm. These results indicate that genetically-modified TMVs are promising templates for the construction of optical metamaterials.