A system and method for operating a machine whereby a workpiece is held on a worktable of the machine with a suction force. When the work piece has a surface area insufficient to receive a full cut from a tool mounted in a tool head of the machine, the machine automatically adjusts the depth and the cutting speed of the tool to lesson the cut so the workpiece is not moved or ejected from the worktable. The depth and speed of the tool may be adjusted in a single cut pass of the tool or they may be adjusted in successive cut passes.