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The following is not an exhaustive of all available software, but systems we've used with FlexScan3D.
Scan Processing Tools (Free)
Rapidform Basis Scan Data Viewing - One of the best tools on the market as a pure viewer
Points To Poly's Mesh Surfacing - Can only handle FlexScan3D's smaller point clouds. (outsmall.asc)
Scanalyze Mesh Alignment, Good results but difficult to use.
TriMesh2 Convert between PLY and Obj, Mesh alignment. (Command Line)
MeshLab Mesh Viewing / Cleanup
MetroCompare meshes
Scan Processing Tools (Not Free)
These are all commercial tools most include a full pipeline to take your point cloud straight to a finalized mesh with all the bells and whistles needed. Each tool has different performance characteristics. The higher end systems tend to have more features.
Industrial Strength - Any of these has the ability to fully process FlexScan3D point cloudsTopology Processing Tools (3D Graphics)
A raw 3D scan mesh is not suitable for use in 3D graphics. They need to a usable topology that's smaller that can be be UV'ed and animated. Most 3D packages will allow you to work inside their package but there are also dedicated tools that assist in this process.
Topogun Specialized re-topology program to polygonsTopology Processing Tools (CAD/CAM)
CAD/CAM needs are different than 3D Graphics. So they have different specialized packages to process the data in to surfaces and solids.
Rapidform XORGeneral 3D Modeling Packages (3D Graphics)
Some artists perfer to use their favorite modeling package and manually draw on top of the mesh. This can often work just as well as a specialized package if you're a master at that tool.
3D Studio Max