For the past month, I've had between fifteen and one-hundred fifteen giant sequoia seeds sitting in damp coffee filters in the dark. I realize now that there's no guaranteed way to prevent mold growth, so rather than freak out, I spent tonight cleaning all of my seeds, and transplanting them in new coffee filter baggies.
I found the best way to do this was to place the seeds in a metal vegetable strainer with very fine holes (less than 1mm square), and run room-temperature water through them. For the few seeds that had a decent build-up of mold, I carefully gave them a little rub, and more water. I used toothpicks to help maneuver the seeds, discarding them after touching dirty ones. I didn't want to waste my time cleaning the seeds, only to give them back their mold afterwards.
Once the seeds are in the soil and sprout, the air circulation should help prevent mold problems at that point. My goal is to keep them as clean as I can until then, then make sure to remove the seedlings from the greenhouse as soon as they sprout. With germination taking anywhere from seven to ninety days, the baggie method really helps fight mold. If I had planted the seeds in soil from day one, there would have been a serious mold problem in the greenhouse pretty early on.