So the basic process is deeply laser etch the panel with the protective paper in place. Paint though this protective paper mask. You can be as sloppy as you like. Then simply peal the paper away. Now you have super clean highly detailed etchings, and the paint is protected because it's actually recessed into the plastic. (That's why you use a deep etch.) You can use any color or combination of colors you like.
Step 1: Deeply etch the design with a surface mask in place.
Step 2: Paint the parts of the design
You can use any color you like, and paint different areas different colors, etc. Here you can see me making a set of gear dials with different colored accent lines. I'm sorry this doesn't match the previous image of what I was laser etching. I wasn't originally trying to document this process, so I didn't take a picture of every step. Jim said I should make an instruactable about it though, so I am, minus the original laser etching/cutting image.