Nanofabrication with finely focused ion and electron beams is reviewed, and position and size controlled fabrication of nano-metals and -semiconductors is demonstrated. A focused ion beam (FIB) interface attached to a column of 200keV transmission electron microscope (TEM) was developed. Parallel lines and dots arrays were patterned on GaAs, Si and $SiO_2$ substrates with a 25keV $Ga^+-FIB$ of 200nm beam diameter at room temperature. FIB nanofabrication to semiconductor specimens caused amorphization and Ga injection. For the electron beam induced chemical vapor deposition (EBI-CVD), we have discovered that nano-metal dots are formed depending upon the beam diameter and the exposure time when decomposable gases such as $W(CO)_6$ were introduced at the beam irradiated areas. The diameter of the dots was reduced to less than 2.0nm with the UHV-FE-TEM, while those were limited to about 15nm in diameter with the FE-SEM. Self-standing 3D nanostructures were also successfully fabricated.