Spin coating has recently been explored as a method for creating multilayer crystal arrays from colloidal suspensions and has demonstrated potential for various applications including optical materials (Jiang et al., 2004, Journal of the American Chemical Society 126(42) 13778). To evaluate the possibility of broad application of this method, we use confocal microscopy to investigate the effects of strain, and reduced stress on local crystallinity of 3D arrays assembled by spin coating. Charge stabilized, refractive index matched poly (12-hydroxystearic acid) stabilized poly(methyl methacrylate) colloids of size about one micron were synthesized and suspended in the viscous solvent dioctyl phthalate and charges were screened with the addition of tetrabutylammonium chloride. To quench assembled structures for interrogation by 3D confocal microscopy, the suspensions (colloid volume fraction ~ 0.35) are spin coated on glass substrates with a small fraction of photopolymer that is subsequently gelled by UV exposure. Upon initiating spin coating, we find that excess suspension is expelled to the outside edge of the substrate by centrifugal forces, resulting in a thin, microscopically level film with complex, spatially varying crystallinity. The full thickness of the colloidal crystal array is imaged at a number of radial positions using confocal microscopy and particle centroids are located in 3D by means of quantitative image processing. Local crystallinity is quantified by application of local bond order parameter criteria developed by ten Wolde et al. (ten Wolde et al., 1996, Journal of Chemical Physics 104 9932). We found local ordering produced by spin coating to be a function of both local reduced critical stress and macroscopic strain. Crystalline structures form when the local reduced stress is of magnitude O(1) or higher and macroscopic strain is >=2. Peclet number was manipulated by varying radial position, spin speed and particle size.