A method for imaging a surface of a substrate using a multi-beam imaging system includes: modifying an electron beam using a multipole-field device; generating beamlets from the electron beam using a beam-splitting device having multiple apertures; in response to projecting foci of the beamlets onto the surface, driving the beamlets using a deflector set to scan a region of the surface for receiving signals based on electrons scattered from the region; and determining an image of the region for inspection based on the signals. The multi-beam imaging system includes: an electron source; a first multipole-field device for beam shaping and beam aberration correction; a beam-splitting device; a projection lens set; a deflector set; an objective lens set; a detector array; a second multipole-field device; a processor; and a memory storing instructions to determine an image of the region for inspection based on the signals.