Methods of aligning a number of physical layers to a pattern formed via multi-patterning are disclosed. A method may include determining a misalignment vector between a first layer and a second layer used to form a pattern via multi-patterning. The method may also include calculating, based on the misalignment vector between the first layer and the second layer, a center position of the pattern. Further, the method may include aligning a third layer to center position of the pattern. A computing system and a processing system are also described.