1. A method of processing a wafer comprising: receiving a wafer, wherein the wafer comprises a plurality of dies, each die having a patterned bi-layer mask thereon, wherein the bi-layer mask includes a soft mask layer and a hard mask layer; creating a pre-processing measurement map using measured metrology data for the wafer including metrology data for at least one isolated bi-layer structure on the wafer, metrology data for at least one nested bi-layer structure on the wafer, or mask data; calculating a first pre-processing prediction map for the wafer based on the pre-processing measurement map, the first pre-processing prediction map including a first set of predicted measured data for the plurality of dies on the wafer; calculating a pre-processing confidence map for the wafer, the pre-processing confidence map including a set of confidence data for the plurality of dies on the wafer, wherein the confidence data is determined using a difference between the first pre-processing prediction map and historical data; determining a prioritized measurement site when the confidence data for one or more dies is not within the confidence limits; and creating a new measurement recipe that includes the prioritized measurement site.