I would soak them in a mix of 10 parts water to one part bleach. You can use a clean brush (one just for tank use) to scrub, but it shouldn't take much . Rinse very very well, then re-soak over-night in water with a good dechlorinator.
Then you can clear coat them. Also, as was suggested, reducing feeding, light time and increasing water changes will keep them clean.
And before anybody even starts something, yes, I do use this bleach mix myself for many things, including soaking my nets. I have yet to lose a fish.