The fabrication of an extended three-dimensional nanostructure with dimensions much larger than the feature size using a focused ion beam is described. By milling two identical patterns of pores with a designed diameter of 460 nm in orthogonal directions, a photonic crystal with an inverse woodpile structure was made in a gallium phosphide single crystal. The patterns are aligned with an unprecedented accuracy of 30 nm with respect to each other. The influence of GaP redeposition on the depth, shape, and size of the pores is described. A literature study revealed that the redeposition of GaP during milling is more pronounced than that of Si found in previous studies. An explanation for this phenomenon is given.