A method and apparatus for controlling a positioning mechanism comprising a smaller scale positioning mechanism for moving a tool within a smaller scale work space and a larger scale positioning mechanism for changing a position of the smaller scale work space within the larger scale work space. A commanded position for the tool is received by a processor unit. An error component is determined using a difference between the commanded position and a current position of the tool in the larger scale work space. A restoring component configured to move the tool toward a selected position in the smaller scale work space is determined. Control signals for controlling the smaller scale positioning mechanism and the larger scale positioning mechanism together to move the tool from the current position to the commanded position are generated using the error component and the restoring component.