Homebrew PCBs

Hi guys, I have now set my plotter up for scratch-etching (carbide 
tipped modified plotter pen)
I am not able to understand how to get the plotter to scratch though 
a resist to expose copper to etch away and isolate tracks.
I have Eagle (free version) and Proteus PCB software packages...
What is the process to go from a PCB in gerber or hpgl to an HPGL 
code file that will trace the outlines of the tracks??

thanks, PK