Aspects of the present disclosure provide a wafer bonding system, which, for example, can include a wafer bonding tool configured to bond a first wafer and a second wafer to each other in accordance with a first wafer bonding recipe to produce a first post-bond wafer, a metrology tool integrated with the wafer bonding tool, and a tool controller coupled to the wafer bonding tool and the metrology tool. The metrology tool can be configured to measure a physical parameter of the first wafer. The physical parameter of the first wafer representing information relates to topographical features of the first wafer. The tool controller can have a model of a wafer bonding process. The model can include an input indicative of the physical parameter of the first wafer and configured to generate the first wafer bonding recipe based, at least in part, on the physical parameter of the first wafer.