An intraoral scanning system for generating a three-dimensional volumetric model of a subject's teeth, the system comprising: a hand-held wand having at least one image sensor and a plurality of light sources (109-111), wherein the light sources are configured to emit light at a first spectral range and a second spectral range, wherein the second spectral range is within near-infrared (near-IR) range of wavelengths; and one or more processors operably connected to the hand-held wand, the one or more processors configured to: capture 3D surface model data of at least a portion of the subject's teeth as the hand-held wand of the intraoral scanner is moved over the teeth; receive a plurality of images into the teeth using light in the second spectral range as the hand-held wand of the intraoral scanner is moved over the teeth so that multiple images of a same internal region of the teeth are imaged; receive, for each of the plurality of images into the teeth, a position of the image sensor of the hand-held wand relative to the subject's teeth; and form the 3D volumetric model of the subject's teeth including internal features by projecting each point of a grid of points corresponding to a volume of the tooth onto the plurality of images using a first calibration, and using the plurality of images and the position of the image sensor relative to the subject's teeth. a hand-held wand having at least one image sensor and a plurality of light sources (109-111), wherein the light sources are configured to emit light at a first spectral range and a second spectral range, wherein the second spectral range is within near-infrared (near-IR) range of wavelengths; and one or more processors operably connected to the hand-held wand, the one or more processors configured to: capture 3D surface model data of at least a portion of the subject's teeth as the hand-held wand of the intraoral scanner is moved over the teeth; receive a plurality of images into the teeth using light in the second spectral range as the hand-held wand of the intraoral scanner is moved over the teeth so that multiple images of a same internal region of the teeth are imaged; receive, for each of the plurality of images into the teeth, a position of the image sensor of the hand-held wand relative to the subject's teeth; and form the 3D volumetric model of the subject's teeth including internal features by projecting each point of a grid of points corresponding to a volume of the tooth onto the plurality of images using a first calibration, and using the plurality of images and the position of the image sensor relative to the subject's teeth. capture 3D surface model data of at least a portion of the subject's teeth as the hand-held wand of the intraoral scanner is moved over the teeth; receive a plurality of images into the teeth using light in the second spectral range as the hand-held wand of the intraoral scanner is moved over the teeth so that multiple images of a same internal region of the teeth are imaged; receive, for each of the plurality of images into the teeth, a position of the image sensor of the hand-held wand relative to the subject's teeth; and form the 3D volumetric model of the subject's teeth including internal features by projecting each point of a grid of points corresponding to a volume of the tooth onto the plurality of images using a first calibration, and using the plurality of images and the position of the image sensor relative to the subject's teeth. <EOS>