We present a micropatterning method for the automatic transfer and arbitrary positioning of computer-generated three-dimensional structures within a substrate. The Gerchberg-Saxton algorithm and an electrically addressed spatial light modulator (SLM) are used to create and display phase holograms, respectively. A holographic approach to light manipulation enables arbitrary and efficient parallel photo-patterning. Multiple pyramidal microstructures were created simultaneously in a photosensitive adhesive. A scanning electron microscope was used to confirm successful replication of the desired microscale structures.