Imho filtering and SEO do not go together.
The filtering application is a tool, aiming at advancing the user experience.
It is usually complex/heavy and creates a lot of pages with identical content.
Look the filtering apps (including their urls) of amazon, ebay, google, etc. They are totally crap in terms of SEO.
In short i see more problems than gains in that approach.
My suggestion is to let the search engines crawl your main product pages (categories, manufacturers).
If you are going to use a filtering extension, make sure that it uses canonical tags pointing those pages, in it's results and use no-follow for it's links.
Otherwise you will end up with a bunch of duplicate content in the search results.