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We describe here a means of improving pattern placement accuracy in the electron-beam lithographic manufacture of membrane masks. Our method is based on collection of the beam transmitted through the membrane with a detector fixed to the mask assembly. A fiducial grid overlaid onto the detector is used to provide a global reference for measurement of the beam position during lithographic patterning. We give results from recent experiments with components of such a system, and estimate 1σ accuracy in our method to be on the order of 1.5 nm. We discuss the effect of beam scattering on our technique, and possible improvements in our implementation.