A system for precisely locating an absolute position of a target structure disposed at a known relative position on a substrate, where the substrate has devices in a pattern. Input means receive information, including a substrate size, a pattern offset, a device size, the known relative position of the target structure, and a target structure shape. Staging means receive the substrate in a known orientation. Processing means are used to locate several positions. A center position of the substrate is located from the substrate size and the known orientation of the substrate. A first intermediate position is located by combining the center position of the substrate with the pattern offset. A second intermediate position is located by combining the first intermediate position with at least a first component of the device size. A third intermediate position is located by combining the second intermediate position with the known relative position of the target structure. The absolute position of the target structure is located by comparing the target structure shape to shapes of structures disposed on the substrate in proximity to the third intermediate position, and aligning the target structure shape to a closest matching one of the structures disposed in proximity to the third intermediate position.