In this paper, we present two methods for registering desired defect lattices within background periodic lattices through spatial light-modulator-based holographic lithography. In the first method, the diffraction efficiency from the engineered phase pattern was used to locally modify the fill fraction of polymerized materials in holographic structures, and, at the same time, we achieved the lattice matching between modified and background regions. In the second method, we registered spatially variant lattices for a 90 deg bend within the background periodic lattices through two steps of phase engineering of the laser beam.