Yes, you can buy filter floss in bulk sizes, or you can buy ordinary thick quilt batting by the yard at almost any fabric store. Make sure you get the kind that does NOT have any antimicrobial treatment added to it as that would kill off your filter bacteria.
Usually the antimicrobial stuff costs a dollar or two more a yard than the kind that hasn't had this added to it. My local fabric store would give me a 40% discount on this stuff if I bought an entire bolt of it. That's about 20 yards, I think. Enough to last me a lifetime and where in heck would I even put the bolt
But keep an eye out for sales.. you can often get it half price, buy several yards and that will last you a very, very long time. The quilt batting has the surfaces slightly bonded together, they use heat to do it, and so they are easy to cut to size, and stick together better than loose pillow stuffing will.