Electronics

PCB Milling Master Class Part 4: Machining, Auto-Leveling, and The "Flip"

By The Maker Team • November 26, 2025
PCB Milling Master Class Part 4: Machining, Auto-Leveling, and The "Flip"
PCB Milling Master Class Series:

The design is done. The G-Code is ready. Now comes the moment of truth.

Milling a PCB is different from milling wood or aluminum. The tolerances are microscopic. If your machine is off by 0.05mm (the thickness of a hair), you might cut too deep and ruin the board, or cut too shallow and fail to isolate the traces.

In Part 4, we are covering the physical workflow. We will cover the "Tape & Glue" fixture method, the critical importance of Height Mapping, and how to execute the double-sided flip using the files we created in Part 3.

Step 1: Fixturing (The Super Glue Method)

Do not use clamps. Clamps bow the PCB material, causing uneven cuts. For PCBs, you need the board to be perfectly flat against the wasteboard.

The "Blue Tape" Trick
  1. Put a layer of Blue Painters Tape on your CNC wasteboard.
  2. Put a layer of tape on the back of your Copper Clad board.
  3. Apply CA Glue (Super Glue) and activator spray to the tape on the wasteboard.
  4. Press the Copper Clad down firmly for 10 seconds.

This holds the board with incredible strength but peels off easily when done, leaving no residue on your machine.

Step 2: The Secret Sauce (Height Mapping)

Here is the reality: Your board is not flat. Even if it looks flat, it likely bows by 0.1mm or 0.2mm. Since we are only cutting 0.05mm deep, this bow will ruin your print.

To fix this, we use Auto-Leveling (Height Mapping). Most hobby CNC software (like Candle, UGS, or bCNC) supports this.

  1. Attach a probe clip to your V-Bit and a wire to the copper surface.
  2. In your control software, select "Create Height Map."
  3. The machine will touch the board in a grid pattern (e.g., every 5mm).
  4. The software creates a 3D map of the warpage and automatically adjusts your G-Code on the fly.
Do not skip this step! 90% of failed PCB mills happen because the user skipped height mapping.

Step 3: Milling the Top Layer

Load the files we created in FlatCAM. We start with the Top Layer (since we haven't flipped the board yet).

  1. Insert your V-Bit (e.g., 20-degree or 60-degree).
  2. Zero your Z-Axis using the paper method or a touch probe.
  3. Run the Height Map.
  4. Run `4_Top_Isolation.nc`: Watch as the machine traces the copper.

Once the traces are cut, do not move the board yet!

Step 4: The Alignment Holes

Before we flip the board, we need to drill the holes that will ensure the back matches the front.

  1. Swap to a 3.0mm Drill Bit (or whatever size alignment pin you chose).
  2. Re-zero your Z-Axis.
  3. Run `1_Alignment_Drills.nc`.
  4. This will drill two holes through the board and into your wasteboard.

Step 5: The Flip

This is the magic trick.

  1. Remove the PCB from the tape.
  2. Find two dowel pins (or even the shanks of old broken drill bits) that fit your alignment holes.
  3. Place the pins into the holes in the wasteboard.
  4. Flip your PCB over (like turning a page in a book) and slide it onto the pins.
  5. Secure the board down again (Tape & Glue works, or clamps if you are careful near the edges).

Your board is now physically mirrored, exactly matching the digital mirror we did in FlatCAM!

Step 6: Milling the Bottom & Drilling

Now that the board is flipped:

  1. Run Height Map Again: The board sits differently now, so map it again.
  2. Run `2_Bottom_Isolation.nc`: This cuts the back traces.
  3. Run `3_Drills_Mirrored.nc`: This drills all the component holes.
  4. Run `5_Cutout.nc`: Finally, cut the board loose from the frame.

Troubleshooting Common Issues

Problem Likely Cause Solution
Copper not cutting through Board is warped / Z-Zero is too high Re-run Height Map or lower Z-Zero by 0.02mm.
Traces are too thin / gone Cut depth too deep Your V-bit gets wider the deeper it goes. Raise Z-Zero.
Fuzzy edges (Burrs) Dull bit or wrong speed Use a new bit or increase spindle RPM. Use a Scotch-Brite pad to clean it up later.

You did it! Pop the board out, sand off the tabs, and give it a quick scrub with steel wool. You now have a professional-grade, double-sided PCB made in your own garage.

In the final part of our series, we will cover Assembly and Soldering, including tips for soldering on bare copper (which is different from commercially tinned boards).

? Back to Part 3