Abstract: An alignment or overlay target that has an optically opaque layer disposed between the top and bottom target structure is measured using opto-acoustic metrology. A classifier library is generated for classifying whether an opto-acoustic metrology signal is on or off the bottom structure. A target may be measured by acquiring opto-acoustic measurement data for the bottom structure of the target and determining a location of the bottom structure using opto-acoustic metrology data acquired from the different locations over the bottom structure and the classifier library. Locations for acquisition of the data may be based on classification results of each measurement and a search pattern. The top structure of the target may be optically imaged. The relative position of the top structure with respect to the bottom structure is determined using the opto-acoustically determined location of the bottom structure and the image of the top structure.