An intraoral scanning system, the system comprising: a hand-held wand having at least one image sensor and a light source configured to emit light at a spectral range within near-infrared (near-IR) range of wavelengths; a display output; a user input device; and one or more processors operably connected to the hand-held wand, display output and user input device, the one or more processors configured to: display a three-dimensional model of a patient's dental arch on the display output; display a viewing window (1003, 1005) over a portion of the 3D model of the patient's dental arch on the display output; change a relative position between the viewing window (1003, 1005) and the 3D model of the patient's dental arch based on input from the user input device; identify, from both the 3D model of the patient's dental arch and a plurality of images of the patient's dental arch taken from different angles and positions relative to the patient's dental arch, a near-IR image taken at an angle and position that approximates a relative angle and position between the viewing window and the 3D model of the patient's dental arch; and display the identified near-IR image taken at the angle and position that approximates the angle and position between the viewing window and the 3D model of the patient's dental arch. a hand-held wand having at least one image sensor and a light source configured to emit light at a spectral range within near-infrared (near-IR) range of wavelengths; a display output; a user input device; and one or more processors operably connected to the hand-held wand, display output and user input device, the one or more processors configured to: display a three-dimensional model of a patient's dental arch on the display output; display a viewing window (1003, 1005) over a portion of the 3D model of the patient's dental arch on the display output; change a relative position between the viewing window (1003, 1005) and the 3D model of the patient's dental arch based on input from the user input device; identify, from both the 3D model of the patient's dental arch and a plurality of images of the patient's dental arch taken from different angles and positions relative to the patient's dental arch, a near-IR image taken at an angle and position that approximates a relative angle and position between the viewing window and the 3D model of the patient's dental arch; and display the identified near-IR image taken at the angle and position that approximates the angle and position between the viewing window and the 3D model of the patient's dental arch. display a three-dimensional model of a patient's dental arch on the display output; display a viewing window (1003, 1005) over a portion of the 3D model of the patient's dental arch on the display output; change a relative position between the viewing window (1003, 1005) and the 3D model of the patient's dental arch based on input from the user input device; identify, from both the 3D model of the patient's dental arch and a plurality of images of the patient's dental arch taken from different angles and positions relative to the patient's dental arch, a near-IR image taken at an angle and position that approximates a relative angle and position between the viewing window and the 3D model of the patient's dental arch; and display the identified near-IR image taken at the angle and position that approximates the angle and position between the viewing window and the 3D model of the patient's dental arch.