A printed circuit board (PCB) with a non-flat surface is very common in radio frequency applications. For this reason, we have designed and produced a PCB milling machine capable of milling a PCB with a non-uniform flatness. Method: By embedding the suggested machine with a G-code reconstruction software, the milling device is programmed to implement the following tasks: Step 1, the machine executes the probing procedure to generate the PCB’s Heightmap; Step 2, the machine transforms the input probing signal to a surface map which is a 2-dimensional grid, Step 3, When the machine is running, the height of the drill tip is adjusted according to the PCB surface flatness condition, and the machine before the actual milling operation. As a result, the proposed machine is capable of milling elastic and unlevelled PCBs at high speed with height differences ranging up to 150mm and an ability to halt when the plane angle varies severely. The proposed machine has been used to fabricate microwave print circuits. A close agreement has been obtained between the measured and simulated S-parameters. Although the machine works properly and is equipped with all basic safety functions, it only costs around US$1500 while the market price of a related German product is about US$70000. Conclusion: A machine able to mill microwave PCBs with an uneven surface and equipped with safety function has been successfully built at the Vietnamese - German University a cost of US$1500, which is far less than the market price of similar ones.