Overlay metrology on bonded wafers

A metrology system for characterizing a sample formed from a first wafer and a second wafer bonded at an interface with a metrology target near the interface may include a metrology tool and a controller. The metrology tool may include one or more illumination sources and an illumination sub-system to direct illumination from the one or more illumination sources to the metrology target, a detector, and a collection sub-system to collect light from the sample. The light collected from the sample may include light from the metrology target and light from a top surface of the first wafer, and the collection sub-system is may direct the light from the metrology target to the detector. The controller may execute program instructions causing the one or more processors to generate estimates of one or more parameters associated with the sample based on data received from the detector.