Three dimensional packaging schemes take advantage of multiple substrate materials, functionality, and reduced area constraints. Alignment of stacks of wafers becomes difficult as the number increases. We investigate full-wafer self-alignment as a means for solving this problem. To date, capillary self-alignment has only been accomplished with tiny, millimeter-sale, objects. Here, wafer-level self-alignment is demonstrated with capillary alignment forces, and we describe several needed, nontrivial advances and considerations compared to the chip alignment. The patterning scheme and the alignment force character are found to be crucial to ensure alignment at the wafer scale. Avoidance of alignment at local minima with the use of multiple length scales, prevention of upper wafer dragging by balancing the wafer and using engineered flow channels, and increased pattern features at small misalignments to combat the decreased alignment force are all discussed. A capture range of a few millimeters in position and several degrees in rotation for the self-alignment is achieved by patterning a hydrophobic self-assembled monolayer. These advances for large structure self-alignment offer a path forward for self-assembly of wafer stacks or other complex, large structures useful for mmWave, 5G antennas, for example. The scheme is compatible with a bonding scheme using the bonding precursor as the alignment fluid.