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Electron projection lithography (EPL) is one possible successor to conventional optical lithography. One type of EPL mask, namely a SCALPEL mask, consists of a large array of rectangular membranes on a 200 mm silicon support wafer. An image of a die is formed by scanning and stitching the patterns resident on the membrane array. Mask CD uniformity must be addressed for a single membrane and for the entire array. Key areas of concern include temperature uniformity during the resist post exposure bake process, heating issues during resist exposure, fogging effects caused by electron scattering from the mask chuck and biasing resulting from the pattern transfer of the mask scattering layer. The purpose of this paper is to address these issues.