The embodiments provided herein disclose a charged panicle beam inspection apparatus. According to an aspect of the invention, there is provided a charged-panicle tool configured to generate a plurality of sub-beams from a beam of charged particles and direct the sub-beams downbeam toward a sample position, the tool charged-particle tool comprising; at least three charged-particle-optical components; a detector module configured to generate a detection signal in response to charged panicles that propagate upbeam from The direction of the sample position; and a controller configured to operate the tool in a calibration mode; wherein: the charged-particle-optical components include: a charged-particle source configured to emit a beam of charged particles and a beam generator configured to generate the sub-beams; and the detection signal contains information about alignment of at least two of the charged-particle-optical components, the at least two of the charged-particle optical components comprising two or more charged-particle optical elements comprising an array of apertures.
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