A method for imaging a surface of a substrate using a multi-beam imaging system, comprising: 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, wherein the substrate is placed on a substrate stage controllable to move the substrate for scanning in at least one of a step-and-scan mode and a continuous scan mode, and wherein when the substrate stage is controlled to move in the step-and-scan mode, the beamlets are driven to scan the region when the substrate stage settles, and when the substrate stage is controlled to move in the continuous scan mode, the beamlets are driven to scan the region when the substrate stage moves at a constant speed in a stage motion direction, characterized in that modifying the electron beam using the multipole-field device further comprises: receiving the electron beam from an electron source, wherein a cross section of the electron beam has a round shape during the step-and-scan mode; and modifying the electron beam using the multipole-field device for beam shaping and beam aberration correction, wherein the cross section of the electron beam is modified from the round shape during the step-and-scan mode into an elliptical shape during the continuous scan mode. 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, wherein the substrate is placed on a substrate stage controllable to move the substrate for scanning in at least one of a step-and-scan mode and a continuous scan mode, and wherein when the substrate stage is controlled to move in the step-and-scan mode, the beamlets are driven to scan the region when the substrate stage settles, and when the substrate stage is controlled to move in the continuous scan mode, the beamlets are driven to scan the region when the substrate stage moves at a constant speed in a stage motion direction, characterized in that modifying the electron beam using the multipole-field device further comprises: receiving the electron beam from an electron source, wherein a cross section of the electron beam has a round shape during the step-and-scan mode; and modifying the electron beam using the multipole-field device for beam shaping and beam aberration correction, wherein the cross section of the electron beam is modified from the round shape during the step-and-scan mode into an elliptical shape during the continuous scan mode. receiving the electron beam from an electron source, wherein a cross section of the electron beam has a round shape during the step-and-scan mode; and modifying the electron beam using the multipole-field device for beam shaping and beam aberration correction, wherein the cross section of the electron beam is modified from the round shape during the step-and-scan mode into an elliptical shape during the continuous scan mode.