Several photogrammetry softwares such as Photomesh or ContextCapture offer the possibility to use a a polygon source to add constraints to the mesh reconstruction, this feature is mostly used to flatten water surfaces to avoid geometrical artifacts (ripples, pits, etc.).
This feature is great when dealing with a large project, correcting by hand (deleting and filling back) is too time consuming and could be avoided by the use of pre existant digitized polygons and their elevation data.