I have been working on this very issue. My aim is to create scaled models in real world coordinates. To perform this task, the point clouds must be cleaned, scaled, and rotated. Here is what I know so far:
1) MeshLab will read ply and x3d files. MeshLab will also display the RGB color values. MeshLab will not permit the editing of individual points. It does not appear possible to get XYZ values of individual points. Scale and rotation transformations can be
performed in MeshLab. I will have to check again, but I believe that MeshLab provides a mechanism to measure the distances between individual points.
2) Blender will import ply files but the color information is lost. Blender permits the deletion of points. I have found that the OFF file format works well, but again color information is lost. In order to measure the distances between points, one must
use the caliper tool.
3) ScanView will open xyzrgb files, but the header row must be removed. The coordinates of individual points can be retrieved. Users must pay for additional functions.
4) VRMesh Studio opens ply files and displays the rgb colors. There are tools for deleting points. The coordinates of individual points can be queried, and the distances between points can be measured. The demo only runs for 30 days.
5) I have been able to open XVZRGB files with software called Copan. It appears to have tools for performing coordinate transformations based on control points. I have not yet tried this out. I am integrating a point cloud as we speak.
It appears that there are no free or open source tools for cleaning orienting the point clouds. I would really like to see either MeshLab or Blender work, but both fall short in some very significant ways.
If someone has any other ideas as to how to perform these tasks, I would be very grateful if that information was posted here.