Most Cam programs let you mix 2D and 3D cutting strategies in the same G-code file.
For instance making a 3d sign you would want Holes for mounting, possibly counterbored. Then you'd have 3D relief and possibly V carving for Txt. Next you'd want to cutout the profile shape. Having 5 separate G-code files doesn't make sense so it's common to combine all the operations into one G-code file.

The example above would have 5 operations, Drilling, Pocketing, 3D relief, V carving, Profile. Could be reduced to 4 if you used pocketing for the holes.

What have you been looking at.?