A method of operating a part cleaning machine includes removably attaching a part to a part holder. A selected first one of a plurality of tools is transferred from a tool holder to a tool chuck to perform a desired cleaning operation. The selected first one of the tools is positioned in a pre-defined tool cleaning position by moving a chuck holder along an axis on a tool positioning plane. The part is positioned in a pre-defined part cleaning position by at least one of moving a cradle along an X axis, rotating the cradle about a first cradle axis, or rotating the part holder about a second cradle axis. The desired cleaning operation is performed on the part with the selected first one of the tools, with the part in the pre-defined part cleaning position and the selected first one of the tools in the pre-defined tool cleaning position.