data3D = Import[file, "VertexData"]; Graphics3D[Point[data3D]]
How to find concave polygon for separated small clusters.
The procedure I suggested for your other "concave hull" question seems to work reasonably well here, simultaneously isolating the clusters and creating the surfaces.
The clusters using this method are just sets of connected polygons. We can build a graph of these connections and use
As I said before, there really isn't such a thing as a concave hull. What you want to do is plot your clusters here.
The first problem involves a machine vision problem known as 3D segmentation. Mathematica doesn't have any tools out of the box to do this, as far as I know.
One way is to guess how many "clusters" are in your data, although that's hard to say because it appear to be sort of fractal. You should experiment with heuristics for doing this.
I guessed about 40 for your data:
You might also try a different metric, although it makes clustering slower:
If you want something besides the convex hull for each cluster, you might try adapting an answer to Finding a Concave Hull.