Ge nanodot formation on Si surface and its three dimensional alignment is investigated using a reduced pressure chemical vapor deposition (RPCVD) system. By exposing GeH4 on Si (001) surface at 550C, a smooth wetting Ge layer is deposited for the first-0.9 nm, and then Ge nanodot formation occurs as Stranski-Krastanov growth mechanism. The Ge nanodots are randomly distributed with density of ~6xl010 cm'2. By postannealing at 600C, the Ge nanodots are coalesced. The size and density become-60 nm diameter 5 nm height and ̃1.5xl010 cm-2 respectively. By exposing GeH4 followed by postannealing at 600C on checkerboard mesa structured Si surface which is fabricated by embedded body-centered tetragonal (BCT) Sio.6Geo.4 nanodot, the Ge nanodot formation occurs at concave regions of the checkerboard mesa. By repeating Ge nanodot deposition and Si spacer deposition by two step epitaxy using SiRt at 600C and using SirfeCh at 700C, vertical alignment of the Ge nanodots is observed. The lateral periodicity of the Ge nanodots is the same as that of the BCT Sio.6Geo.4 nanodot template. The driving force of the self-ordered alignment is tensile strain of Si spacer surface above the Ge nanodots.