A custom-built surface sol-gel pumping system was built for applying conformal sol-gel based coatings with controlled thicknesses on three-dimensional (3-D) nanostructured templates. The 3-D templates utilized in this work were derived from biological species, such as diatoms and butterfly wings, as well as a synthetic photoresist polymer (SU-8). Tin oxide coatings were applied on silica-based diatom frustules using the automated surface sol-gel pumping system. An organic dendrimer method was developed for amplifying hydroxyl groups on the silica-based frustule surfaces to enhance the surface sol-gel deposition process. Conformal tin oxide coatings with controlled thicknesses were obtained on the hydroxyl amplified frustule surfaces; however, little if any deposition was observed on the frustules that were not subjected to the hydroxyl amplification process. The automated surface sol-gel system was also utilized to apply multicomponent tin oxide-doped titania alkoxide chemistries on the wing scales of a blue Morpho butterfly. The alkoxide solutions reacted directly with the OH functionalities provided by the native chitin chemistry of the scales. The tin oxide served as a rutile nucleating agent which allowed the titania to completely crystallize in the high refractive index rutile titania phase with doping concentrations of tin oxide as low as 7 mol % after annealing at 450oC. The tin oxide-doped titania coatings were both nanocrystalline and nanothick and replicated the nanostructured scales with a high degree of precision. Undoped titania coatings applied on the scales required a heat treatment of 900oC to crystallize the coating in the rutile titania phase which led to adverse coarsening effects which destroyed the nanostructed features of the scales. Tin oxide-doped titania coatings were also deposited on 3-D SU-8 photonic crystal structures. The coating was crystallized in an acidic solution at 80oC which led to the formation of rutile titania inverse opal photonic crystal structures which maintained the overall structure and ordering of the template. Barium titanate and europium-doped barium titanate coatings were applied on diatom frustules using a conventional reflux/evaporation deposition process. The silica-based diatom frustules had to first be converted into magnesia/silicon composite replicas using a gas/solid displacement reaction to render the template chemically compatible with the barium titanate-based coating. Conformal titanate-based coatings were obtained on the magnesia frustule replicas possessing uncontrolled thicknesses and excess inorganic particles using the reflux/evaporation deposition process. The europium-doped barium titanate coated frustules exhibited bright red photoluminescent properties upon stimulation with an ultraviolet light source.