With regards to your etching you will need to select the any shape command, you then enter the shape co rodinate corners so if you want to remove a square area starting at the top left that would x1, y1, then move to the right corner x2 y2 then down to the bottom right x3 y3, bottom left x4, y4 and finally back to the top left to complete the etch.
There is an extract command for material thickness which allows you to immediately fin the thickness of any material. The values are in Angstrons so remember 10A = 1nm
The ATHENA and ATLAS documentation discuss all of these issues in more detail but I hope that helps.
Regards, Ken.