We present two methods for characterization of wafer bonding. They are based on recess and mesa bond test structures with various shapes, measurement of unbonded regions using scanning acoustic microscopy (SAM), and image analysis. The first method maps locally the surface energy across the bonded wafers using the measured deformations around these structures and the finite element method (FEM). The FEM analysis is supported by analytical modeling. The second method uses the measured bonding probabilities of 10-19 nm deep recess bond test structures in investigation of surface interactions and in determination of the average of the surface energy at the wafer level. The present methods and proposed optimized test structures allow the evaluation of surface cleans without destructive, off-line methods such as the crack-opening method, which is employed as a reference. The methods are utilized in the investigation of the effect of O2 and N2 plasma activation and the dilution and temperature of Standard Clean 1 on Si/SiO2 direct bonding. The results from both methods correlate with each other. The bond strength of the annealed wafers is observed to increase in the order 1) O2 plasma, 2) standard SC1 at 65°C, 3) N2 plasma, and 4) dilute SC1 at 45°C.