The simple answer is that you need to mount your boards vertically. Pulling this off requires 1) a vertical clamping fixture and 2) a CNC that allows you to mill beyond the boundary of the bed. Here are a few resources to give you the idea:
- A video of CNC end joinery in action.
- An exotic example of what can be done with it.
- If you’re really curious then an hour-long SIG discussion.
There’s much to learn about this but the results can be really beautiful.
Few software focus on this capability but JointCAM is worth checking out.
That said, the fancy stuff in the video above was all done in VCarve Pro.