A new approach for fabricating arrays of electron beam columns by stacking silicon wafers with micron accuracy has been developed. This approach combines the precision of semiconductor processing and fiber optic technologies. A (100) silicon wafer is anisotropically etched to create an array of apertures on the top or bottom of the wafer and four orthogonal v- grooves on both surfaces of the wafer. Precision pyrex fibers align and bond the v-grooves on the top of one wafer to the bottom of the next wafer. This procedure is repeated to create thick structures and a stack of six wafers is used to create arrays of scanning electron microscopes (SEMs). This technique is suitable for fabricating 1 - 30 mm long electron optical columns. The optimum size is determined by the desired array size, operating voltage, resolution, field of view, and working distance. The first wafer contains an array of micromachined field emission electron sources. The next three wafers accelerate and focus the electron beams. The last two wafers in the stack have electrodes to deflect each beam and correct for astigmatism. The performance of an SEM improves as its length is reduced and a subcm 2 keV SEM with a field emission source should have approximately 7 nm resolution.