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Nanotopography, which refers to surface height variations of tens to hundreds of nanometers that extend across millimeter-scale wavelengths, is a wafer geometry feature that may cause failure in direct wafer bonding processes. In this work, the nanotopography that is acceptable in direct bonding is determined using mechanics-based models that compare the elastic strain energy accumulated in the wafer during bonding to the work of adhesion. The modeling results are presented in the form of design maps that show acceptable magnitudes of height variations as a function of spatial wavelength. The influence of nanotopography in the bonding of prime grade silicon wafers is then assessed through a combination of measurements and analysis. Nanotopography measurements on three 150-mm silicon wafers, which were manufactured using different polishing processes, are reported and analyzed. Several different strategies are used to compare the wafers in terms of bondability and to assess the impact of the measured nanotopography in direct bonding. The measurement and analysis techniques reported here provide a general route for assessing the impact of nanotopography in direct bonding and can be employed when evaluating different processes to manufacture wafers for bonded devices or substrates.