Occasionally, you might wish to remove a joint from the listed joints in Milkshape, yet there seems no clear way to delete them.
It’s not too obvious, but it IS easy once you know how: simply double-click the joint you wish to delete, then press the DELETE key on your keyboard.
Vóila! Your Milkshape joint has been deleted.
References: Object Creation Part 1: The Beginner’s Guide To Meshing
