1. A method comprising: receiving, by a processing device, data from an intraoral scan of a patient responsive to performance of the intraoral scan being performed by an intraoral scanner, the data comprising a plurality of intraoral images of a dental site; receiving, by the processing device, an indication that at least two intraoral images of the plurality of intraoral images comprise a representation of less than an entirety of a non-rigid adhesive object that was affixed to the dental site at a target area, wherein the non-rigid adhesive object has known properties comprising a known two-dimensional (2D) surface pattern and at least one of a known thickness, a known size, a known shape or a known color, wherein the non-rigid adhesive object provides a reference point for image registration, wherein the at least two intraoral images comprise a first intraoral image comprising a representation of a first portion of the known 2D surface pattern that is not shown in a second intraoral image and the second intraoral image comprising a representation of a second portion of the known 2D surface pattern that is not shown in the first intraoral image, the first intraoral image being non-contiguous with the second intraoral image, and wherein the non-rigid adhesive object partially deforms based on a shape of the target area, wherein partial deformation of the non-rigid adhesive object deforms at least one of the known shape or the known 2D surface pattern; performing, by the processing device, pattern recognition to identify the non-rigid adhesive object having the known 2D surface pattern in the at least two intraoral images; extrapolating a shape and orientation of the non-rigid adhesive object in the first intraoral image based on the representation of the first portion; performing, by the processing device, image registration between the at least two intraoral images using the non-rigid adhesive object identified in the at least two intraoral images, wherein the image registration between the first intraoral image and the second intraoral image is performed using the extrapolated shape and orientation of the non-rigid adhesive object in the first intraoral image; generating a three-dimensional model of the dental site based on the image registration; determining a surface of a base of the non-rigid adhesive object that has been partially deformed based on the known properties of the non-rigid adhesive object and the partial deformation of the non-rigid adhesive object; subtracting the representation of the non-rigid adhesive object from the three-dimensional model based on the known properties of the non-rigid adhesive object; and interpolating a surface of a portion of the dental site where the non-rigid adhesive object was located based on a) data for other portions of the dental site and b) the surface of the base of the non-rigid adhesive object.