According to one aspect of the invention, a semiconductor substrate processing apparatus and a method for processing semiconductor substrates are provided. The method may include providing a semiconductor substrate having a surface and a plurality of features on the surface, each feature being positioned on the surface at a first respective point in a first coordinate system, plotting the position of each feature at a second respective point in a second coordinate system; and generating a translation between the first and the second coordinate systems. The generating of the translation may include calculating an offset between the first and the second coordinate systems. The calculating of the offset may include calculating an offset distance between a reference point of the first coordinate system and a reference point of the second coordinate system and calculating an offset angle between an axis of the first coordinate system and an axis of the second coordinate system.