Remove the roughing skin on vertical surfaces
The cutting length of your finishing cutter may be too short
An important feature in 3D CAM software is the option to offer separate operations for Roughing and for Finishing (as shown for instance in this tutorial video). For a roughing operation DeskProto offers extra functionality, including the option to machine in roughing layers (cannot be switched off for the first operation) and the option to leave a roughing skin around the part, to be removed when finishing. After such roughing operation the finishing cutter can simply follow the surface of the geometry, without the need for layers.
This process works fine for most geometries. Though not for all: for a geometry with high vertical surfaces the roughing skin can cause a problem for the finishing operation.

Three parts, each with a roughing skin, and a finishing cutter with its cutting length shown.
For the leftmost part finishing with this cutter is fine,
for the other two parts the cutting length is too short to remove the roughing skin.
For the leftmost part finishing with this cutter is fine,
for the other two parts the cutting length is too short to remove the roughing skin.
The image above shows three parts (drawn in brown). After the roughing operation each part is a bit too large as the roughing skin still is present (drawn in pink). That skin will be removed by the finishing cutter (drawn in grey). The advantages of this process are that inaccuracies in the roughing toolpath will be removed when finishing, and that the resulting surface will be very smooth as the workload for the finishing cutter is very low.
The exception just mentioned occurs in case of an (almost) vertical surface. The finishing cutter will follow the geometry, removing the skin. No problem as the skin is only a thin layer of material. However, the image also shows what happens when a high vertical surface is present: the finishing cutter tries to remove all skin on this vertical surface in one toolpath. As result the shaft of the cutter will hit the material: a collision (drawn in red) !
Such vertical surface can be present in the geometry (the part in the center) or when the cutter travels far below the geometry (the rightmost part), for instance when machining a part from two sides.

Roughing toolpaths and finishing toolpaths for a sphere, with extra waterline toolpaths in-between.
The solution for this problem is to create an extra operation, between roughing and finishing.
Such semi-finish operation needs to be without roughing options and use the waterline strategy.
For this extra operation as said no roughing skin needs to be set, and no roughing layers either. Strategy for this operation is Waterline, with detail settings "Top to bottom" and a Waterline distance that is smaller than the cutting length of the cutter. As you can see in the image above this is a very efficient way to remove the roughing skin from the vertical surfaces that are present.

Simulations of the result, after running the three sets of toolpaths shown above.
The red marker shows the start of the vertical surface, that no longer causes a problem now.
The red marker shows the start of the vertical surface, that no longer causes a problem now.
These simulations show the result after each of the toolpaths has been run. The leftmost simulation clearly shows the original problem, indicated with the red marker. Here the first finishing toolpath would try to remove the roughing skin over this complete height. In one movement of the cutter. Which is not possible, as the cutter does not have cutting edges over this complete height: as a result the shaft of the cutter would have hit the material. The extra set of waterline toolpaths has prevented that.