The image above shows both a scan and 3d Design (height shaded) in the same coordinate space. Only scans and designs that are in exactly the same coordinate system can be compared.
To regroup a scan based on its perpendicular distance to a design model, start by clicking the Group by DTM button from the Point Cloud Tools tab.
The tools pane on the right of the screen will show something similar to that below.
Set the Model to the appropriate source. Note OBJ, FBX and STL files can be used as well as the triangles from a Model.
Change the Max Distance of the first band to the delta you want to use. 0.005 in this case. Then press "Adds Band". The name will change and the max and min distances of the next band will update. Repeat this enough times to cover the tolerance you want. In this case its been done up to 25-30mm.
Make sure to turn off the "Vertical Distance" option, or the process will not work properly.
Press Apply, and n4ce will create the new Groups and process the scan data.
When it's finished, turn off the Groups that are not needed, and change the Display Mode of the point cloud to "Group Colours".