A variable focus laser machining system is disclosed. The machining system may have a laser emitter configured to emit a laser beam. Additionally, the machining system may have a focusing element configured to focus the laser beam. The machining system may also have a controller. The controller may be configured to focus the laser beam at a first focal point. The first focal point may be approximately positioned on a first machining surface of a work piece. The controller may also be configured to determine that the first machining surface has moved relative to the first focal point. Additionally, the controller may be configured to re-focus the laser beam at a second focal point. The second focal point may be positioned between a second machining surface and a predetermined surface spaced apart from the second machining surface.