E-beam lithography with alignment gating

The present disclosure provides one embodiment of a reflective electron-beam (e-beam) lithography system. The reflective e-beam lithography system includes an e-beam source to generate an e-beam; a digital pattern generator (DPG) having a plurality of pixels that are dynamically and individually controllable to reflect the e-beam; a substrate stage designed to secure a substrate and being operable to move the substrate; an e-beam lens module configured to project the e-beam from the DPG to the substrate; and an alignment gate configured between the e-beam source and the DPG, wherein the alignment gate is operable to modulate an intensity of the e-beam.