If you are using a milling machine to produce the boards you may have the files you need at this point, or you may have some file manipulations to do first. But when the board comes out of the milling machine it is done ( assuming the milling machine does the drilling as well, and of course you may need to trim the board to size as well )
But maybe you are using “toner transfer”. In this case you print the image of the file on paper and then use heat to transfer the design to the board. There are a bunch of different ways to do this, at the simple end just a clothes iron, at the work well end us a lamina tor. The board is then placed in a chemical enchant to remove the unwanted copper.
Somewhat like toner transfer is using special boards coated with an optically sensitive etchant resist material. You print a negative of your design on a clear material and expose the negative and board to the right kind and amount of light. The board is then developed and ready to go into the enchant. If you mess up this step you can clean up the board and have a bare board, perhaps you can re coat with the optical resist.
You can also use spray paint as a resist. Remove it by using a laser cutter in etch mode.
* Two sided PCB using toner method – http://www.instructables.com/id/Two-sided-PCB-using-toner-method/
* Cheap and Easy Toner Transfer for PCB Making – http://www.instructables.com/id/Cheap-and-Easy-Toner-Transfer-for-PCB-Making/
* How to make 2-sided Printed Circuit Boards -- http://www.instructables.com/id/How-to-make-2-sided-Printed-Circuit-Boards/
* How to make a printed circuit board (PCB) using the UV light LED method. -- http://www.instructables.com/id/How-to-make-a-printed-circuit-board-PCB-using-th/
* UV LED Exposure Box – http://www.instructables.com/id/UV-LED-Exposure-Box/
* Simple UV lightbox for PCBs – http://www.instructables.com/id/Simple-UV-lightbox-for-PCBs/