Lithographic apparatuses suitable for, and methodologies involving, complementary e-beam lithography (CEBL) are described. In an example, a method of fine alignment of an e-beam tool includes projecting an electron image of a plurality of apertures of an e-beam column over an X-direction alignment feature of a wafer while moving the wafer along the Y-direction. The method also includes detecting a time-resolved back-scattered electron (BSE) detection response waveform during the projecting. The method also includes determining an X-position of every edge of every feature of the X-direction alignment feature by calculating a derivative of the BSE detection response waveform. The method also includes, subsequent to determining an X-position of every edge of every feature of the X-direction alignment feature, adjusting an alignment of the e-beam column to the wafer.