If you've removed the primary filter (the small, plastic one with a screen in it, in the engine bay), running it will only clog the secondary filter. The secondary is a finer filter, and will catch the particles that would have gotten stuck in the primary anyways (it's also more expensive). The primaries are easier to change out and cheaper.
The biodiesel will help clean out everything, but everything that it cleans out will end up in your filters anyways. It'll get cleaned out eventually, you'll just have an interesting time
