Process

The process of creating a PCB with a CNC mill includes the following steps:

Design a circuit with the KiCad Schematics editor
Design the board layout with the KiCad PCB editor
Route the traces, possibly with an Autorouter (freerouting)
Export the Gerber files from the PCB editor
Generate the gcode for the isolation milling and the drill holes with pcb2gcode
Autolevel the physical board with cnc.js
Create the traces by isolation milling with cnc.js
Drill the holes with cnc.js

Software

KiCad (installation and usage)
freerouting (installation and usage)
pcb2gcode (installation and usage)
cnc.js (installation and usage)

Board Layout with PCB Editor

Isolation milling depends upon the possible precision that can be achieved with a given CNC machine, routing bit, etc. If the trace width and the clearance are selected too narrow, then the isolation milling process may not succeed. Values such as trace width and the clearance can be modified in the board setup dialog. Here are the default values:

boardSetup_01

In my case, the following values work:

boardSetup_02

You can check the correct routing by running a design rules check:
Go to Inspect -> Design Rules Checker

designRules_01

Export Gerber files from PCB Editor

Go To File -> Fabrication Outputs -> Gerbers (.gbr)

gerber_plot_01

Click on Generate Drill Files...

gerber_drill_01

Converting gerber files to gcode

The easiest way to use pcb2gcode is to put a file named millproject into the same folder where the gerber files are, and simply call

pcb2gcode

Contents of millproject file

Example of millproject file: millproject
Example for content: https://reprap.org/wiki/PCB_Milling#pcb2gcode

G81 command and GRBL

The G81 command is for a drill cycle where you state the Z-axis once and then only list the X and Y movement
implying that for each X and Y line, a Z-axis lowering will happen.
GRBL controllers do not support this command, and the bit will just move around without lowering the Z-axis.

For CNC controllers which do not support these so-called "canned cycles", you can disable the G81 option in the millproject file:

# Drill options
nog81=true

Negative Coordinates

pcb2gcode will by default place the backside of a PCB on the negative side of the X-Y-plane.
If you prefer to have your board to have positive Coordinates, you can add the lines for the offset option to the millproject file, for example :

x-offset=-65 mm
y-offset=5 mm

Drill Holes

The following applies to through-hole components.

Pre-Drilling

You may get better results in creating drill holes by putting a small indent with the milling bit on the point where a drill will be used later:

predrill

Run pcb2gcode with the following parameter in the millproject file:

#predrill
zdrill=-0.05000

Run the gcode with the resulting drill gcode file.

Don't forget to apply the saved autolevel results to this gcode file before running it.

Drill Sizes

To reduce the number of tool changes, find the component with the largest pin diameter and use a drill that is a bit larger,
For example

Name	Image	measured size
blue trim pot		0.45 mm
IC Socket		0.56 mm
DIP switch		0.58 mm
Arduino pin		0.60 mm

To drill the holes, change the tool by removing the milling bit and inserting the drill bit. Make sure to zero out the drill bit before starting the drilling.