Imaging spectroscopy (hyperspectral imaging) data have mainly been used to map surface materials covering relatively small areas from airborne sensors over the past 20+ years. As part of the U.S. Geological Survey Integrated hyperspectral, geophysical and geochemical studies of Yellowstone National Park hydrothermal systems project, we have collected multiscale imaging spectrometer data including borehole core, field, and airborne data. These data give us the unique opportunity to map subsurface and surface alteration of shallow epithermal systems at scales ranging from microns to meters per pixel. Airborne Visible and Infrared Imaging Spectrometer (AVIRIS), Corescan HCI-3, HySpex VNIR-1800 and SWIR-384 imaging spectrometers, and a Riegl VZ-2000i terrestrial lidar system were used in this study. Maps utilizing spectral analysis of multiscale hyperspectral data indicate the presence of mineral assemblages consistent with epithermal deposits. Minerals such as alunite, hydrated silica, and kaolinite typically form in steam-heated cap systems and can be found in core and AVIRIS data. At depth, higher temperature fluids that are less acidic produce mixed-layer kaolinite with clay/muscovite and then montmorillonite and muscovite towards the bottom of the borehole. This transition can be seen in AVIRIS and field data at the Grand Canyon of the Yellowstone and in borehole Corescan data at Y-12 Norris-Ii R874. Instrument specifications, collection parameters, and setup for data acquisition will be discussed as well as mapping software and preliminary results.