An apparatus for making variable diameter and shape holes through metal plates in a sheet plate machining gantry machine comprises two parallel cross members and two horizontal parallel guides integral with the cross members and supporting a horizontal cross arm which is controllably driven on the guides, the horizontal arm supporting horizontal parallel guides therealong is controllably driven an apparatus including a milling tool which can controllably driven in a vertical plane. The method comprises the step of controllably simultaneously driving a two-fluted mill both in a vertical plane (Z), and in a horizontal plane (U).