1. A non-transitory computer-readable memory medium that has program instructions stored thereon, wherein the program instructions are executable by a computer system to implement a method comprising: displaying a first image in a first window using a display system, wherein the first image corresponds to a first view of a graphical object set that includes one or more graphical objects in a three-dimensional (3D) space, wherein each of the one or more graphical objects represents a corresponding sub-surface geological structure; displaying a second window using the display system; generating a polygon in the 3D space, wherein said generating includes: receiving user input defining a closed planar polyline in the second window, wherein said user input is supplied by a user drawing the closed planar polyline in the second window and includes a first set of drawing inputs to the second window, wherein the closed planar polyline includes three or more 2D vertices in the second window; and mapping each of the three or more 2D vertices to a respective 3D point in the 3D space, thereby obtaining three or more 3D points that define 3D vertices for the polygon; rendering the polygon with respect to the first view to generate an update for the first image; displaying the updated first image in the first window, wherein the updated first image depicts at least a portion of the polygon and at least a portion of a first of the graphical objects of the graphical object set; wherein the first graphical object includes a mesh that covers a surface in the 3D space, wherein the three or more 3D points reside on said surface, wherein the method further comprises: receiving user input indicating that a boundary of the polygon represents an unconformity between a first facies and a second facies; generating a new mesh for the surface, wherein the new mesh includes a first submesh and a second submesh that interface along the polygon boundary, wherein the first submesh corresponds to the exterior of the polygon, wherein the second submesh corresponds to the interior of the polygon, wherein at least a portion of the first submesh is assigned to the first facies, wherein the second submesh is assigned to the second facies; and assigning a property value consistent with the second facies to grid points of the second submesh.