With a height map, your CNC should easily compensate depth of cut for variations in PCB flatness. Take a look at how this works.
Most cheap printed circuit board material is covered by 1 ounce of copper per square foot. You will find this provides a nominal copper thickness of 0.035 millimetres. Surprisingly this is the width of a human hair. Normal manufacturing tolerances mean that you might find variation between 31-35 μm.
So, when you make your PCB using traditional etching, the chemicals have to eat away very little copper to create the desired circuit. We are all used to seeing the solution turn green as the etching proceeds. Then, you have to consider how to dispose the remaining toxic sludge.
With isolation milling, you don’t need to worry about chemicals, but PCB flatness becomes the major issue. The copper layer sits on a board of either phenolic cotton paper (FR-2) or woven glass or epoxy (FR-4). Most boards today are FR-4, but FR-2 is a bit easier to cut with a V-bit. Wearing your dust mask is a good idea while milling. I am also using a bit of mineral oil as a cutting and dust collecting fluid.
When milling, you are trying to separate 30 μm traces of copper by carving a channel around 100 μm deep. But when you test the PCB flatness, you will find that your board is not actually flat. Surface variability for a typical board is easily 100 μm in itself, as shown above.
Fortunately, your CNC can easily compensate for this lack of PCB flatness that you will encounter almost every time.
PCB Flatness – Using a Height Map
Shown above is an actual height map created by Candle GRBL Controller using an electric probe. Controllers will probe the circuit board by lowering the Z (vertical) axis until a complete circuit is made between the tool and the copper surface. This feature is built in to most recent firmware versions of GRBL. By the way, GRBL does not actually stand for anything; it’s just a name.
In the height map, the red sections are high and the blue sections are low.
When you are milling, the software raises the depth of cut on the red sections, and lowers it accordingly on the blue parts. The result should be a 100 μm cut regardless of actual PCB flatness.