The operator of a computer numerical control (CNC) milling machine will use a CNC language like G-code to program the machine. After the operator inputs the G-code instructions into the CNC controller, the machine will move the cutting tool and the workpiece at predetermined intervals and speeds.
FreeCAD will produce G Code. So you start with FreeCAD, design the object, then export
the Gcode. Many will use programs to account for bed leveling in CNC, like Flatcam,
which modifies the GCODE by probing the object or cnc bed, then modifying all the GCODE
Z axis dimensions.
Just to add to the above, a good reference to G-code programming is "CNC Programming Handbook" by Peter Smid.
Also there are what is know as CAD/CAM "Computer Aided Manufacturing" programs , which will produce the G-code etc for entering in to the machine.
A CNC machine Operator should also posses machining skills in order to select tooling and feed-rates etc.