Fluorescent milled nanodiamonds are one of the most promising physical bases for quantum devices. The nitrogen vacancy (NV) center in diamond acts a room temperature, optically addressable quantum system which significantly decreases the infrastructure costs of developing quantum devices. Since nanodiamonds are nontoxic and colloidally stable, the nanoparticles are particularly attractive to the fields of sensing and nanomedicine where environmental changes must be detected with nanoscale resolution. Particle to particle irregularity, however, alters the spin and optical properties of each nanodiamond and complicates their integration into more complex systems. In this dissertation, we address the inhomogeneity of nanodiamonds and provide multiple paths towards fully utilizing these quantum emitters. First, we develop a technique for the self-assembly of nanodiamonds into arrays. We then utilize these arrays to perform a statistical study of the nanodiamonds and characterize the impact of the material’s surface and crystalline structure on the NV center’s optical and spin properties. Next, we establish a surface modification method that both improves the general properties of the nanodiamonds and enables chemical conjugation reactions. Together, these results deliver a newfound level of control and uniformity over an otherwise uncontrollable and polydisperse material.