The whole Process is called "Reverse Engineering".
FreeCAD has a "Reverse Engeneering" Workbench.
Your Scanner will first try to locate the outer surfaces of your objects and will then store
the coordinates of measured points in 3D Space in a "point cloud" data structure.
The next step would be to create a mesh (or even a meshed object) from this data.
for example can be used to do this. Here
is a Tutorial for that and here
The resulting File is often an STL-File.
[I don't know at the moment if FreeCAD has features to do that as well ...]
Making editable Features in a CAD application is the next step in this "Reverse Engineering" Process.
Some commercial CAD's have quite intelligent (and expensive) Sub-Modules for that.
is an interesting Thread about this topic.
Hope this post provides some starting points for you.