Alignment control of three dimensional (3D) SiGe nanodot arrangements is investigated using a reduced pressure chemical vapor deposition system. Several cycles of SiGe layers with 30% Ge content and Si spacers are deposited by SiH 4 -GeH 4 at 550 °C and SiH 4 or SiH 2 Cl 2 at 700 °C, respectively, to form a 3D SiGe nanodot structure. By using SiH 4 as a precursor for the Si spacer deposition, SiGe nanodots are aligned at staggered positions resulting in a body-centered tetragonal (BCT) structure, because a checkerboard mesa structured Si surface is formed and the next SiGe nanodot formation occurs at the concave region to reduce surface energy. On the other hand, after planarizing the Si surface with checkerboard structure by chemical mechanical polishing (CMP), the new SiGe nanodot formation occurs directly above the embedded SiGe nanodot located nearest to the Si surface (dot-on-dot). The driving force seems to be local tensile strain formed at the Si surface above the embedded SiGe nanodot. By using SiH 2 Cl 2 as precursor for the Si spacer deposition, a smooth Si surface can be realized on BCT SiGe nanodot structures without CMP process resulting in a vertically aligned SiGe nanodot formation. The local tensile strain formation in Si above SiGe nanodots is confirmed by nano beam diffraction analysis.