When you first start cutting with your Industrial CNC Router, you may find that some parts of your design are deeper than others. This isn't anything to be alarmed about and just means that you need to plane the surface of your tabletop.
If you have a T-Slot tabletop, obviously you can't plane the aluminum, so the best option is to plane your sacrificial tabletop (a sheet of mdf, or other material, placed on your tabletop to prevent cutting into your table.)
First, make sure the sacrificial material is attached securely to the tabletop. I recommend double sided tape on the underside. This is to make sure that when you plane the surface, that sections won't lift up, because the planing made them lighter.
You'll then want to insert a fly cutting bit.
In your Vectric Post Processor program, make a rectangle the size of your sacrificial sheet and tell it to "pocket" the inside.
Post the G-Code and open it in your Mach 3 to surface your table.
Keep the file somewhere easy to find as you may want to run it again when your sacrificial board gets worn with use.