I use coffee filters during my Rue brews and extractions, they work fine. I usually filter each boil from the Rue seed (as i pour each boil off into a big pot), then boil/reduce down the brew, add a little vinegar, filter once more and then i toss in 10 grams of Sodium Carbonate per 400mls of brew, stir it in and filter after 30 minutes.
In my experience with Rue, the first base will be brown, then i redissolve it in/stir it into warm vinegar water, then i filter out anything that won't dissolve, re-base with Sodium Carbonate and the second base will be golden or a little white. Then i redissolve/stir it in again, filter, re-base it again, and this time the color is white. I do it a few more times to make it purer, and then filter em' off one last time to let em' dry overnight.
The next day they should be dry enough to scrape off of the coffee filter using a butterknife, into a container, and then i use the butterknife to mash the flakes of extract into powder and let it dry a little more. Once they're good and dry, they can be used
Tip number one, after every filtering, i usually take the filter and wet it a little with tap water, and ring it back out into the brew or extract-liquid. This ensures you get as much of the extract as possible.
Tip number two, while filtering, i usually take a spoon and repetitively tap the strainer that the coffee filter is in, as it allows the liquid to flow through faster/better but i don't usually do that on the last couple of basings as the liquid is clear enough for the liquid to drain out leaving the nice white extract behind.