Far-field spectral imaging, coupled with computer vision methods, is demonstrated as an effective inspection method for detection, classification, and root-cause analysis of manufacturing defects in large area Si nanopillar arrays. Si nanopillar arrays exhibit a variety of nanophotonic effects, causing them to produce colors and spectral signatures which are highly sensitive to defects, on both the macro- and nanoscales, which can be detected in far-field imaging. Compared with traditional nanometrology approaches like scanning electron microscopy (SEM), atomic force microscopy (AFM), and optical scatterometry, spectral imaging offers much higher throughput due to its large field of view (FOV), micrometer-scale imaging resolution, sensitivity to nm-scale feature geometric variations, and ability to be performed in-line and nondestructively. Thus, spectral imaging is an excellent choice for high-speed defect detection/classification in Si nanopillar arrays and potentially other types of large-area nanostructure arrays (LNAs) fabricated on Si wafers, glass sheets, and roll-to-roll webs. The origins of different types of nano-imprint patterning defects—including particle voids, etch delay, and nonfilling—and the unique ways in which they manifest as optical changes in the completed nanostructure arrays are discussed. With this understanding in mind, computer vision methods are applied to spectral image data to detect and classify various defects in a sample containing wine glass-shaped Si resonator arrays.