Modern high-throughput nanopatterning techniques, such as nanoimprint lithography, make it possible to fabricate arrays of nanostructures (features with dimensions of 10's to 100's of nm) over large area substrates (cm2 to m2 scale) such as Si wafers, glass sheets, and flexible roll-to-roll webs. The ability to make such large-area nanostructure arrays (LNAs) has created an extensive design space, enabling a wide array of applications including optical devices, such as wire-grid polarizers, transparent conductors, color filters, and anti-reflection surfaces, and building blocks for electronic components, such as ultracapacitors, sensors, and memory storage architectures. However, existing metrology methods will have trouble scaling alongside fabrication methods. Scanning electron microscopy (SEM) and atomic force microscopy (AFM), for instance, have micron scale fields of view (FOV) that preclude comprehensive characterization of LNAs, which may be manufactured at m2 per minute rates. Scatterometry approaches have larger FOVs (typically 100's of µm to a few mm), but traditional scatterometry systems measure samples one point at a time, which also makes them too slow for large-scale LNA manufacturing. In this work, we demonstrate parallelization of the traditional spectroscopic scatterometry approach using hyperspectral imaging, increasing the throughput of the technique by a factor of 106-107. We demonstrate this approach by using hyperspectral imaging and inverse modeling of reflectance spectra to derive 3-dimensional geometric data for Si nanopillar array structures over both mm and cm-scale with µm-scale spatial resolution. This work suggests that geometric measurements for a variety of LNAs can be performed with the potential for high speed over large areas which may be critical for future LNA manufacturing.