I have a detailed mesh (600k faces) of a hole in the ground, produced from photogrammetry of a volcanic collapse pit in Hawaii. The mesh surface ends just outside the rim of the pit, but doesn't have any holes inside the pit.
I have two goals:
1) I want to be able to render views where there is a stand-in for the "ground" around the pit, occluding the backfaces of the pit geometry, so that it's immediately obvious where the rim is.
2) I want to end up with a watertight mesh, so that I can 3D print it.
I think what I want to do is inset the pit mesh into one end of a cylinder, similar to doing a boolean subtract between the pit and cylinder; however, since the rim of the pit isn't perfectly flat, I'd like to end up with the final top face of the cylinder going above (and possibly below) its original height to meet up with the edge of the pit mesh (see mockup image).
Note that I'm not married to doing the mesh manipulation in Blender if there's a better option. Also, although my mockup below shows a texture derived from the original photos, I don't intend for the final mesh to use a texture, so don't worry about preserving it.
I've found a partial solution- the current version is good enough for the super-rough renderings I need, although it has enough inverted and otherwise problematic faces that it isn't printable (probably caused by the edge of the mesh being very messy, with a straight line going radially away from any given "edge" vertex possibly passing through another bit of the mesh). Basically, I used the vertices along the edge of the mesh to build a cylinder around the rest of the mesh.
All of the following was done in Edit Mode:
0) A bit of cleanup by selecting the main mesh (select one vertex, hit L), inverting the selection (CtrlI), and deleting the few floating blobs.
1) Select the edge of the mesh (by selecting all non-manifold edges with CtrlAltShiftM). (Trying to select it as an edge loop failed due to the topology not being as clean as Blender likes.)
2) Follow these directions to turn that outer loop of points into a circle:
2a) Flatten the points into a plane: hit S (or click the "scale" button in the Transform panel), left-click to get the number-entry panel to pop up, and set the Z value to 0.
2b) Turn the loop into a circle using the "To Sphere" tool (spacebar and search); use a Factor of 1 to make a perfect circle.
2c) Scale in X and Y to place the circle fully outside the rim of the pit (this can probably be combined with step 2a).
3) Extrude the outer loop to make a cylinder wall (Extrude: Edges Only; use the manual editing panel to set the X and Y offsets to 0 and the Z component to slightly below the bottom of the pit.)
4) Close the bottom of the cylinder with the "extrude and merge edges" solution from this question (E, Escape, ⎇ AltM, A).