Create your model in whatever 3D app you choose. Model the the object that
you would like to be the positive shape and then model the object that you
would like to be negative. Name the negative object _negative and make
it a child of the first object, select both and export as object. Choose
select mesh from the merge parameters and it works.
You can also create a child object in 3D Coat and call that _negative, then
export both as a scene.