Measurement of the relative positions of two objects in three dimensions with sub-nanometer precision is essential to fundamental physics experiments and applications such as aligning multi-layer patterns of semiconductor chips. Existing methods, which rely on microscopic imaging and registration of distant patterns, lack the required accuracy and precision for the next generation of three-dimensional (3D) chips. Here we show that 3D misalignment between two distant objects can be measured using metasurface alignment marks, a laser, and a camera with sub-nanometer precision. Through simulations, we demonstrate that the shot noise-limited precisions of the lateral and axial misalignments between the marks are λ