In this work, we study the use of a spatial light modulator (SLM) for local manipulation of phase in interfering laser beams to fabricate photonic crystal templates with embedded, engineered defects. A SLM displaying geometric phase patterns was used as a digitally programmable phase mask to fabricate 4-fold and 6-fold symmetric photonic crystal templates. Through pixel-by-pixel phase engineering, digital control of the phases of one or more of the interfering beams was demonstrated, thus allowing change in the interference pattern. The phases of the generated beams were programmed at specific locations, resulting in defect structures in the fabricated photonic lattices such as missing lattice line defects, and single-motif lattice defects in dual-motif lattice background. The diffraction efficiency from the phase pattern was used to locally modify the filling fraction in holographically fabricated structures, resulting in defects with a different fill fraction than the bulk lattice. Through two steps of phase engineering, a spatially variant lattice defect with a 90° bend in a periodic bulk lattice was fabricated. Finally, by reducing the relative phase shift of the defect line and utilizing the different diffraction efficiency between the defect line and the background phase pattern, desired and functional defect lattices can be registered into the background lattice through direct imaging of the designed phase patterns.