Can anybody know how to design a PCB using CNC machine?

Look at LPKF.

Seems an expensive way of doing it, but I suppose you could take a single sided board and cut away the copper you don't need.
Precision will be interesting, as you don't want the board to be damaged.
Obviously you can't do multilayered boards.
What's the purpose of the exercise?

You can also do multilayer boards that are milled or laser cut. Look at LPKF. I did my first double sided board 30 years ago with just drill mills. You will need plating tank and press for multilayer.

I think your question is how to design not build. If I am correct, use SPICE software which will help you develop a design and verify it's ability before you build. For CNC operation you may have several boards depending on you intended outcome. I assume you want to add a special application to existing functions or rebuild an existing board. Either way start with SPICE first.