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In this work, a scalable automated approach for fabricating 3D microgranular crystals consisting of desired arrangements of microspheres using holographic optical tweezers and two-photon polymerization is introduced. The ability to position microspheres as desired within lattices of any configuration allows designers to engineer the behavior of new metamaterials that enable advanced applications (e.g., armor that mitigates or redirects shock waves, acoustic lens for underwater imaging, damage detection, and noninvasive surgery, acoustic cloaking, and photonic crystals). Currently, no self-assembly or automated approaches exist with the flexibility necessary to place specific microspheres at specific locations within a crystal. Moreover, most pick-and-place approaches require the manual assembly of spheres one by one and thus do not achieve the speed and precision required to repeatably fabricate practical volumes of engineered crystals. In this paper, the rapid assembly of 4.86 µm diameter silica spheres within differently packed 3D crystal-lattice examples of unprecedented size using fully automated optical tweezers is demonstrated. The optical tweezers independently and simultaneously assemble batches of spheres that are dispensed to the build site via an automated syringe pump where the spheres are then joined together within previously unattainable patterns by curing regions of photocurable prepolymer between each sphere using two-photon polymerization.