Controllable growth of wafer-scale in-plane nanowires (NWs) is a prerequisite for achieving addressable and scalable NW-based quantum devices. Here, by introducing molecular beam epitaxy on patterned Si structures, we demonstrate the wafer-scale epitaxial growth of site-controlled in-plane Si, SiGe, and Ge/Si core/shell NW arrays on Si (001) substrate. The epitaxially grown Si, SiGe, and Ge/Si core/shell NW are highly homogeneous with well-defined facets. Suspended Si NWs with four {111} facets and a side width of about 25 nm are observed. Characterizations including high resolution transmission electron microscopy (HRTEM) confirm the high quality of these epitaxial NWs.