An apparatus which exposes a substrate to radiant energy includes a unit which holds a first mask having a pattern which includes a pattern of a target mark, a unit which projects a pattern of radiant energy to the substrate through the first mask, a unit which holds a second mask having an auxiliary pattern for identifying the target mark to be formed on the substrate, and a unit which controls the projecting unit so as to project a pattern of radiant energy to the substrate through the second mask.