An ion beam apparatus is provided, the ion beam apparatus comprising a movable ion source, a condenser lens, an aperture, and a scanning unit disposed between the condenser lens and the aperture, said scanning unit being adapted to scan an ion beam across the aperture. Furthermore, a method for aligning components of an ion beam apparatus is provided, comprising the steps of: producing an ion beam by means of an ion source, producing a first image of a beam cross section of the ion beam at a first voltage of a condenser lens, producing a second image of the beam cross section of the ion beam at a second voltage of the condenser lens, and positioning the ion source so that the centers of the first and second images coincide.