Alignment of wafers for 3D integration

A method of aligning substrates, comprising:

• (a) at least coarsely aligning a first substrate atop a second substrate;
• (b) determining rotational misalignment between the first and second substrates from overlay measurements obtained by illuminating, through windows in the first substrate, targets of the first substrate and corresponding targets of the second substrate;
• (c) moving at least one of the first or second substrates to address the rotational misalignment;
• (d) determining misalignment in a first direction between the first and second substrates from overlay measurements obtained by illuminating, through windows in the first substrate, targets of the first substrate and corresponding targets of the second substrate;
• (e) moving at least one of the first or second substrates to address the misalignment in the first direction;
• (f) determining misalignment in a second direction between the first and second substrates from overlay measurements obtained by illuminating, through windows in the first substrate, targets of the first substrate and corresponding targets of the second substrate;
• and
• (g) moving at least one of the first or second substrates to address the misalignment in the second direction.

A structure including a plurality of stacked microelectronic elements, comprising:

• a first microelectronic element and a second microelectronic element, the first microelectronic element having a rear surface, a front surface remote from the rear surface, and a plurality of metalized through silicon vias exposed at the rear surface;
• first alignment patterns provided at a rear surface of the first microelectronic element, the first alignment patterns being aligned with exposed ends of the through silicon vias at the rear surface;
• second alignment patterns at the rear surface of the first microelectronic element aligned with the exposed ends of the through silicon vias;
• third alignment patterns exposed at a surface of the second microelectronic element juxtaposed with the rear surface of the first microelectronic element;
• a recess in the first microelectronic element aligned with the first alignment patterns;
• a handle element having a surface attached to a front surface of the first microelectronic element, the handle element having an opening aligned with the first alignment patterns, such that a beam of light can illuminate the first and second alignment patterns through the opening and the recess and a return signal can be obtained therefrom for aligning the first microelectronic element with the second microelectronic element.