A dual beam system includes an ion beam system and a scanning electron microscope with a magnetic objective lens. The ion beam system is adapted to operate optimally in the presence of the magnetic field from the SEM objective lens, so that the objective lens is not turned off during operation of the ion beam. An optional secondary particle detector and an optional charge neutralization flood gun are adapted to operate in the presence of the magnetic field. The magnetic objective lens is designed to have a constant heat signature, regardless of the strength of magnetic field being produced, so that the system does not need time to stabilize when the magnetic field is changed.