You can clear the Boundary Points list in the scan dialog box (Insert | Scan) of any of the scan types by right-clicking while the cursor is inside the Boundary Points list. A Reset Boundary Points button appears. Clicking this button resets all the boundary points to zero and the number of boundary points is set to the minimum for each scan type.
PC-DMIS doesn't allow you to clear the boundary points while you are using the Cut CAD button available on Section scans. In this case, you need to click the Show Bnd button to show the boundary points again before clearing the boundary points.