At the moment this is not possible. The filters work only on categories and immediate subcategories.
We would consider enhancing the filters to work for more than two levels of categories for the next version. However right now we have two really strong arguments against this:
1. We believe that more than two level of categories for an e-commerce web site is not very user friendly and most e-shops try to avoid this. In fact you will rarely see such an organization. However in your case you have your top most category hidden. So I am wondering why this is?
2. The performance implications of having all the products from a category tree to be filtered are enormous. So if we are to implement this it would really have to be well thought of and worth the effort.