A method of direct hybrid bonding first and second semiconductor elements of differential thickness is disclosed. The method can include patterning a plurality of first contact features on the first semiconductor element. The method can include second a plurality of second contact features on the second semiconductor element corresponding to the first contact features for direct hybrid bonding. The method can include applying a lithographic magnification correction factor to one of the first patterning and second patterning without applying the lithographic magnification correction factor to the other of the first patterning and the second patterning. In various embodiments, a differential expansion compensation structure can be disposed on at least one of the first and the second semiconductor elements. The differential expansion compensation structure can be configured to compensate for differential expansion between the first and second semiconductor elements to reduce misalignment between at least the second and fourth contact features.