I think I have figured it out, FINALLY! I have outlined what I did in detail to help anyone else who may be having the same problem. How to define specific areas for copper removal 1) Load gerber file (FILE>OPEN GERBER) 2) In the “Project” tab, select the Gerber object to highlight it 3) Click on the “Selected” tab 4) In the “Non-copper Region” section, set the Boundary Margin (I used 0.2), click on the “Create Geometry” button. A red box appears around the complete circuit board and red lines appear around all traces. This represents all the areas of the board with no copper. 5) In the “Project” tab, highlight the new object (same name as the Gerber, with “_non-copper” added) 6) Click on the “Edit Geometry” button on the top toolbar to activate the drawing tools 7) Select the appropriate tool needed to define the cleared-copper area. I used the square. Then draw the desired area on the circuit. When complete, the selected zone turns blue. 8) Click on the “Update Geometry” button on the top toolbar. The newly defined section turns red. This activates the newly defined section. 9) Click on the “Edit Geometry” button to re-activate the tools and click on the arrow selector tool. 10) First, select the boundary box around the entire circuit. It turns black. This is the complete area of non-copper that our square section will be cut from and it must be selected first. 11) Then, select the defined (square) section for copper removal. It also turns black. The user-defined section functions as a cutting tool and it must be selected second. 12) Click the “Polygon Intersection” button, then click inside the user-defined square region. A new blue box defines the desired copper-removal section with the traces excluded from the selection zone. 13) Click the “Update Geometry” button to finalize the changes. All red lines disappear except the new user-defined zone. This is now the area that will be cleared of copper (except for any traces within the section) 14) Click on the “Selected” tab, go down to the “Paint Area” section. Enter the desired cutting parameters for your CNC tools and click “Generate”. 15) Click inside the defined removal zone, toolpaths will appear with the defined zone, but not over the traces within the zone. For additional defined sections for copper removal, this process must be repeated starting at step #2 above). Each time, it will create an additional _non-copper entry under the “Project” tab. When all desired areas have been defined, you can combine them into 1 object prior to generating and exporting G-code for your CNC. To combine the objects, go to the “Project” tab and select each desired “_non-copper” object while holding down the CTRL key until they are all highlighted. Then go the top toolbar and do EDIT>JOIN GEOMETRY. The new Combo object contains all the selected copper removal zones and can be exported as a single set of G-Code.