Is there a way to perform an XOR function on a single layer? I know how to perform the function on multiple layers however my artwork brings the solder mask in on a single layer and I'd like to XOR this layer.
Use the command "DeEmbed" (menu: Edit / De-Embed). Select all objects on the layer and FAB 3000 will detect all overlapping areas and make them clear or dark (as needed). I noticed you had a DXF file, here's a sample forum link which shows how to perform DeEmbed (i.e boolean operations) on a DXF:
Let me know if that helps.