Engineering plasmonic nanostructures that simultaneously achieve high colloidal stability, high photothermal stability, low non-specific binding to biological specimens, and low toxicity is of significant interest to research in bionanotechnology. Using gold nanorods, we solved this problem by encapsulating them with a multilayer structure, silica, hydrophobic ligands, and amphiphilic-polymers. In comparison with nanorods covered with the conventional surface chemistries, such as surfactants, polyelectrolytes, thiolated polymers, and silica shells alone, the new nanorods remain single in various solutions and show remarkable stability against laser irradiation. We further demonstrated specific targeting and effective treatment of prostate tumor cells using nanorod–aptamer bioconjugates. This exquisitely formulated nanoencapsulation technology could potentially help stabilize other plasmonic nanostructures that are not in the most thermodynamically or chemically stable states, and should open exciting opportunities in nanotechnology-based imaging and therapeutics.