New fabrication methods of various three dimensional (3D) Au nanodot arrays are proposed in this paper. These processes utilize single layer Au nanodot arrays fabricated by the templated thermal dewetting method. Multilayer nanodot array is fabricated by repeating spatter coating of SiO2 layer and Au layer followed by thermal dewetting on a single layer nanodot array. It is confirmed that nanodots are aligned vertically with good regularity. It is also shown that the multilayer nanodot array exhibits strong extinction spectrum due to the Localized Surface Plasmon Resonance (LSPR). Then, a MIM nanodot array is fabricated from a double layer Au nanodot array employing selective etching by reactive ion etching (RIE) technique. Optical property of the MIM nanodot array is discussed, and application to single molecular analysis by Surface Enhancement Raman Scattering (SERS) effect is proposed. Finally, a nanopillar array is fabricated by applying RIE to a single layer nanodot array. It is shown that an Au nanodot is placed on the top of a SiO2 nanopillar.