Your question suggest you're new to solid modeling and mesh modeling. Fusion is really bad at dealing with mesh models. Also, the approaches used for dealing with meshes are entirely different than those used with solid models. I suggest getting mesh mixer and learning how to use it to manipulate meshes, if your going to be dealing with stl's very much. There are a ton of youtube video's on using mesh mixer. The things you learn about mesh files will be relevant even if you later choose to use a different mesh editing software.
That said, you can do what your asking in fusion (though it works better with mesh mixer, which has more tools). The trick is to reverse the normal direction of the faces on your model, and then place it inside of a mesh shape that will be your mold. here's a screen cast (the last step would be to run "make closed mesh" on each half of the result. not always necessary)