Our situation it's next, I have a Magento 1.9 store live and we are developing a new store in Magento 2. New store it's a new clean versión of site and we only have to migrate products, categories and attributes (we don't need orders, for example).
We only have Amasty layered navigation module installed, but if it's a problem we can restore a clean installation.
There's a tool to do this? I can't find if Magento official Data Migration Tool has this option.