Homebrew PCBs

>
>You need a clean area to avoid any dust because of that I don't know 
>whether it is a good idea to use the same machine for drilling/printing

Is to get the speed and precision of the cnc when drilling.
Also to get all on a single machine, using available HPGL or Gerber programs.

>or not. If dust is on the trace, sometimes it becomes a part of 
>resist but if it is between traces then it can create a bridge.

You can drill, vacuum clean, change the drill head with the print one 
and print.
No dust.