An apparatus basically uses a simple and compact multi-axis magnetic lens to focus each of a plurality of charged particle beams on sample surface at the same time. In each sub-lens module of the multi-axis magnetic lens, two magnetic rings are respectively inserted into upper and lower holes with non-magnetic radial gap. Each gap size is small enough to keep a sufficient magnetic coupling and large enough to get a sufficient axial symmetry of magnetic scale potential distribution in the space near to its optical axis. This method eliminates the non-axisymmetric transverse field in each sub-lens and the round lens field difference among all sub-lenses at the same time; both exist inherently in a conventional multi-axis magnetic lens. In the apparatus, some additional magnetic shielding measures such as magnetic shielding tubes, plates and house are used to eliminate the non-axisymmetric transverse field on the charged particle path from each charged particle source to the entrance of each sub-lens and from the exit of each sub-lens to the sample surface.