A system that facilitates precise inter-chip alignment. The system includes a first integrated circuit chip, whose surface has etch pit wells. The system also includes a second integrated circuit chip, whose surface has corresponding etch pit wells that mate with the etch pit wells of the first integrated circuit chip. Spherical balls are placed in the etch pit wells of the first integrated circuit chip such that when the corresponding etch pit wells of the second integrated circuit chip are substantially aligned with the spherical balls, the spherical balls mate with the etch well pits of the second integrated circuit chip, thereby precisely aligning the first integrated circuit chip with the second integrated circuit chip.