According to an embodiment, a method of operating a charged particle beam device is provided. The charged particle beam device includes a beam separation unit, a first optical component distanced from the beam separation unit and a second optical component distanced from the beam separation unit and distanced from the first optical component. The method includes generating a primary charged particle beam. The method further includes generating a first electric field and a first magnetic field in the beam separation unit. The method further includes guiding the primary charged particle beam through the beam separation unit in which the first electric field and the first magnetic field are generated, wherein a travel direction of the primary charged particle beam leaving the beam separation unit is aligned with a first target axis under the influence of the first electric field and the first magnetic field. The method further includes generating a secondary charged particle beam by impingement of the primary charged particle beam onto a sample. The method further includes separating the secondary charged particle beam from the primary charged particle beam in the beam separation unit, wherein the secondary charged particle beam is deflected under the influence of the first electric field and the first magnetic field to travel from the beam separation unit to the first optical component. The method further includes generating a second electric field and a second magnetic field in the beam separation unit. The method further includes guiding the primary charged particle beam through the beam separation unit in which the second electric field and the second magnetic field are generated, wherein the travel direction of the primary charged particle beam leaving the beam separation unit is aligned with the first target axis under the influence of the second electric field and the second magnetic field. The method further includes separating the secondary charged particle beam from the primary charged particle beam in the beam separation unit, wherein the secondary charged particle beam is deflected under the influence of the second electric field and the second magnetic field to travel from the beam separation unit to the second optical component.