A misregistration metrology system useful in manufacturing semiconductor device wafers including an optical misregistration metrology tool configured to measure misregistration at at least one target between two layers of a semiconductor device which is selected from a batch of semiconductor device wafers which are intended to be identical, an electron beam misregistration metrology tool configured to measure misregistration at the at least one target between two layers of a semiconductor device which is selected from the batch and a combiner operative to combine outputs of the optical misregistration metrology tool and the electron beam misregistration metrology tool to provide a combined misregistration metric.