A multiple-tool parameter set configuration and misregistration measurement system and method useful in the manufacture of semiconductor devices including using a first misregistration metrology tool using a first set of measurement parameters to measure misregistration between at least two layers at multiple sites on a wafer, including a plurality of semiconductor devices, the wafer being selected from a batch of wafers including a plurality of semiconductor devices intended to be identical to corresponding semiconductor devices on all other wafers in the batch of wafers, thereby generating a plurality of first misregistration data sets, using a second misregistration metrology tool using a second set of measurement parameters to measure misregistration between the at least two layers at multiple sites on a wafer selected from the batch of wafers, thereby generating a plurality of second misregistration data sets, selecting an adjusted first set of modeled measurement parameters associated with the first misregistration data sets and an adjusted second set of modeled measurement parameters associated with the second misregistration data sets, thereby generating a matched misregistration data set and thereafter measuring misregistration between at least two layers of at least one additional wafer, selected from the batch of wafers, using at least one of the first misregistration metrology tool using the adjusted first set of modeled measurement parameters and the second misregistration metrology tool using the adjusted second set of modeled measurement parameters.