A charged particle beam system is disclosed, comprising: • a charged particle beam generator for generating a beam (8) of charged particles; • a charged particle optical column (226) arranged in a vacuum chamber, wherein the charged particle optical column is arranged for projecting the beam of charged particles onto a target, and wherein the charged particle optical column comprises a charged particle optical element for influencing the beam of charged particles; • a source (62) for providing a cleaning agent; • a conduit (64) connected to the source and arranged for introducing the cleaning agent towards the charged particle optical element; wherein the charged particle optical element comprises: • a charged particle transmitting aperture (46) for transmitting and/ or influencing the beam of charged particles, and • at least one vent hole (60) for providing a flow path between a first side and a second side of the charged particle optical element. Further, a method for preventing or removing contamination in the charged particle transmitting apertures is disclosed, comprising the step of introducing the cleaning agent while the beam generator is active.