Trying to re-create the described problem, we edit the 3D Model:
adding a base height which pushes the model up above the stock height.
If we then go to Toolpaths and assign a 3D Roughing toolpath:
using instead a tight vector around the 3D model:
and then try to create a 3D toolpath:
it is empty as was described as a problem.
Going back to the 3D model:
the red appearance is caused by parts of the 3D model being above the Stock Height.
If we adjust the 3D model so that it is wholly within the stock:
and switch back to the Toolpaths pane:
We see that 3D toolpaths may be assigned, with an end result of:
