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The cyan and magenta lines are for etching. I like to add details and lines to make the models more realistic and to help me remember where to glue on bits that aren't attached to the surface with tabs and holes. How much power to use depends on what laser cutter and material you're using. Typically you'll want to use higher speed and lower effect and frequency, but how much lower effect and frequency depends on how deep you want the laser to etch. I can't help you any further than this, you'll need to refer to your laser cutter's manual for the rest. Typically, you'll find a chart somewhere in the manual with suggestions for cutting and etching different materials. A good rule of thumb for etching is to start with a high speed setting and low power/effect and pulse frequency. If the etching is too weak, you can always do another run with more power or lower speed. I hope you find this helpful. And please post pics on your thingiverse page if you make one of my models. There's nothing more pleasing than to see other people make something you've designed! :)