Free-standing epitaxially grown nanowires provide a controlled growth system and an optimal interface to the underlying substrate for advanced optical, electrical, and mechanical nanowire device connections. Nanowires can be grown by vapor-phase epitaxy (VPE) methods such as chemical vapor deposition (CVD) or metal organic VPE (MOVPE). However, VPE of semiconducting nanowires is not compatible with several microfabrication processes due to the high synthesis temperatures and issues such as cross-contamination interfering with the intended microsystem or the VPE process. By selectively heating a small microfabricated heater, growth of nanowires can be achieved locally without heating the entire microsystem, thereby reducing the compatibility problems. The first demonstration of epitaxial growth of silicon nanowires by this method is presented and shows that the microsystem can be used for rapid optimization of VPE conditions. The important issue of the cross-contamination of other parts of the microsystem caused by the local growth of nanowires is also investigated by growth of GaN near previously grown silicon nanowires. The design of the cantilever heaters makes it possible to study the grown nanowires with a transmission electron microscope without sample preparation.