Sampling nearest distant point from all directions?

[Kwanmok]

My mesh (or point cloud) has several complex shape layers surrounding each other and I would like to remove the exterior layers and only leave a layer that is located inside the structure. The structure is an oyster cluster(groups of shells) and I am trying to isolate a specific interstitial space surrounded by un-wanted meshes(or points).(See attached picture.), Red square is the 3D space I want to extract whereas the yellow-colored areas are the external layers I would like to remove. I have been using scissors from CC or Meshmixer to remove the surroundings and it does some job but still leaves surplus structure around it. I am trying to crop out just the 3D space inside it.

Currently, I was thinking of placing several imaginary points in between the interstitial spaces and from those points, sample points around all directions (like a sphere) only with the nearest distance, so that I won't get any points from the outside mesh.

So, my question is whether there is a way to sample points from all directions and moreover, a way to sample the closest point in a certain direction.