A charged particle beam system is disclosed, comprising: a charged particle beam generator for generating a beam of charged particles; a charged particle optical column 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 for providing a cleaning agent; a conduit 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 for transmitting and/or influencing the beam of charged particles, and at least one vent hole for providing a flow path between a first side and a second side of the charged particle optical element, wherein the vent hole has a cross section which is larger than a cross section of the charged particle transmitting aperture. 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.