A scanning system comprises an intraoral scanner to capture scan data of a dental site and a computing device to generate a 3D rendering of the dental site. The scanner comprises one or more input devices configured to provide manual interaction with the computing device, where: a first activation of the input device(s) causes the scanning system to enter the scan mode, wherein the 3D rendering has a first visualization during the scan mode; and a second activation of the input device(s) causes the scanning system to enter an overlay mode, wherein the 3D rendering has a second visualization during the overlay mode, wherein the computing device is to present a menu comprising menu options on the display while the scanning system is in the overlay mode, and wherein the scanner is usable to select among the presented menu options.