The present invention is directed to a method and system of intelligent dummy filling placement to reduce inter-layer capacitance caused by overlaps of dummy filling area on successive layers. The method and system treats each consecutive pair of layers together so as to minimize dummy filling overlaps between each layer. In particular, dummy fill features on each layer may be placed in a checkerboard pattern to avoid overlaps. As such, the present invention may eliminate large overlap area of the dummy patterns on consecutive layers by utilizing intelligent dummy filling placement.