The thickness of 3-dimensional (3D) mesoporous silica ultrathin films was controlled at a single-nano-meter scale by wet-etching. A drop casting method with an aqueous etchant of ammonium fluoride was effective in etching the surfaces of films in the direction perpendicular to their substrates. The decrease in the film thickness depends on the interface tension of etching solutions. The wettability of thin films also influences the etching. CoPt nanodots were electrodeposited within ultrathin silica films on Ru substrates to form CoPt nanodot patterns.