Gold nanostructures were synthesized by etching away gold from heat-treated mesoporous silica-coated gold nanorods (AuNR@mSiO2), providing an example of top-down modification of nanostructures made using bottom-up methodology. Twelve different types of nanostructures were made using this bottom-up-then-top-down synthesis (BUTTONS), of which the etching of the same starting nanomaterial of AuNR@mSiO2 was found to be controlled by how AuNR@mSiO2 were heat treated, the etchant concentration, and etching time. When the heat treatment occurred in smooth moving solutions in round-bottomed flasks, red-shifted longitudinal surface plasmon resonance (LSPR) was observed, on the order of 10-30 min, indicating increased aspect ratios of the gold nanostructures inside the mesoporous silica shells. When the heat treatment occurred in turbulent solutions in scintillation vials, a blue shift of the LSPR was obtained within a few minutes or less, resulting from reduced aspect ratios of the rods in the shells. The influence of the shape of the glassware, which may impact the flow patterns of the solution, on the heat treatment was investigated. One possible explanation is that the flow patterns affect the location of opened pores in the mesoporous shells, with the smooth flow of solution mainly removing CTAB surfactants from the pores along the cylindrical body of mSiO2, therefore increasing the aspect ratios after etching, and the turbulent solutions removing more surfactants from the pores of the two ends or tips of the silica shells, hence decreasing the aspect ratios after etching. These new stable gold nanostructures in silica shells, bare and without surfactant protection, may possess unique chemical properties and capabilities. Catalysis using heat-treated nanomaterials was studied as an example of potential applications of these nanostructures.