In one embodiment, a first vacuum chamber of an electron beam column has an opening which is positioned along an optical axis so as to pass a primary electron beam that travels down the column. A source that emits electrons is positioned within the first vacuum chamber. A beam-limiting aperture is configured to pass a limited angular range of the emitted electrons. A magnetic immersion lens is positioned outside of the first vacuum chamber and is configured to immerse the electron source in a magnetic field so as to focus the emitted electrons into the primary electron beam. An objective lens is configured to focus the primary electron beam onto a beam spot on a substrate surface so as to produce scattered electrons from the beam spot. Controllable deflectors are configured to scan the beam spot over an area of the substrate surface. Other features and embodiments are also disclosed.