Mesh missing sides after Boolean intersection

Question

Blender newbie here. I am working on some topology models with custom borders, and I'm encountering a problem with Boolean intersection where the sides of the resulting mesh are nonexistent. I come from a solid CAD modeling background, so I'm confused at this problem. I've searched for a couple weeks on what might be causing this, but haven't found answers so far. It's quite possible I just don't know the mesh modeling jargon well enough to ask the right question, but here I am.

My process is as follows:

1. Use a 3D map service to generate a topology STL file with a rectangular footprint.
2. Import topology STL into Blender.
3. Use a custom Python script and KML data to create a PLY point cloud that defines the boundary of the desired footprint. This fits within the original rectangular footprint.
4. Select the point cloud and create a face from all of the points using F hotkey.
5. Extrude the newly created face up and down beyond the minimum and maximum height of the topology STL.
6. Use a Boolean intersection on the original STL, with the extruded custom boundary as the tool.

At this point, the mesh is missing its sides, as in the picture:

I've considered deleting the bottom face and extruding the topology down, but my end goal is a flat bottom face so the model could be 3D printed, so the resulting copy of the topology is yet another problem.

Is there a quick way to either connect the top part of the mesh to the bottom and create the sides, or to get rid of the bottom face and quickly extrude the topology down to a flat face?

Answer 1

Try this:

Delete the bottom face.

Select everything, extrude downward.

Press S Z 0 to flatten the extruded faces on the Z axis.