Alignment marks to enable 3D integration

Disclosed are a structure including alignment marks and a method of forming alignment marks in three dimensional (3D) structures. The method includes forming apertures in a first surface of a first semiconductor substrate; joining the first surface of the first semiconductor substrate to a first surface of a second semiconductor substrate; thinning the first semiconductor on a second surface of the first semiconductor substrate to provide optical contrast between the apertures and the first semiconductor substrate; and aligning a feature on the second surface of the first semiconductor substrate using the apertures as at least one alignment mark.