One embodiment relates to an electron beam apparatus for automated imaging of a substrate surface. An electron source is configured to emit electrons, and a gun lens is configured to focus the electrons emitted by the electron source so as to form an electron beam. A condenser lens system is configured to receive the electron beam and to reduce its numerical aperture to an ultra-low numerical aperture. An objective lens is configured to focus the ultra-low numerical aperture beam onto the substrate surface. Other embodiments are also disclosed.