You also have to remove the protective paper from the top, but when you do this, the soot from the cutting / engravings that are towards the bottom of the sheet ends up on the engravings at the top of the sheet.
It is a real pain to clean.
The solution is a jig made from 1/4" MDF
Step 1: Leave the Paper on -- Then Cut
I would but the parts back into where they were and then etch them. It solved the issue of the burning on the edges, but it still caused a lot of soot tot appear on the parts cumulatively from the bottom.
I came to the conclusion that there had to be a better way to do things.
Step 2: Laser Cut the 1/4" MDF to Your Pattern
I cut both of them to size on the panel saw.
Next, I drilled holes so that I could bolt them together with 1/4"-20 bolts and cut a recess on the bottom using a forestner bit to accommodate the nut.
Next, i created a pattern using Corel Draw were I wanted to locate the parts that will be engraved. It takes a little bit of time to cut through the MDF, but the Trotech Lasers at TechShop will do it. I also cut a 2" hole using the laser to that I can use to push the parts out without having to turn over the board.
Another benefit is that I can use this template to lay out the etching and I am sure that it hits in the right place.
To align the jig, all you have to do it to use the red-dot on the laser and make sure that the laser and the jig are at 0,0.
This makes doing multiple parts a breeze.
I made it at Tech Shop.