A method for fabricating a semiconductor device is disclosed. An exemplary method includes forming a first structure in a first layer by a first exposure and determining placement information of the first structure. The method further includes forming a second structure in a second layer overlying the first layer by a second exposure and determining placement information of the second structure. The method further includes forming a third structure including first and second substructures in a third layer overlying the second layer by a third exposure. Forming the third structure includes independently aligning the first substructure to the first structure and independently aligning the second substructure to the second structure.