Chicks aren't human babies and don't need to be raised in a sterile environment. Even human babies shouldn't, actually. The push towards sanitation and hygiene was a great improvement from the "good" (not) old days when people died of mundane things because of a lack of basic hygiene. But now it's gone too far in the other direction, kids are raised in environments that are too sterile, and their immune systems don't have a chance to develop proper defenses. Chickens, being animals, need even less sanitation than humans. Think about a broody raising her chicks outside - nobody is baking the soil for them, nobody is cleaning anything, they set their little feet on the soil outside as soon as mama takes them out of the nest, and they live under the same conditions as the adult chickens. Now, the difference with a brooder, is that a brooder is much smaller than an outdoor coop and pen (or free range), so poop builds up faster and it gets dirtier per square area than the outside, so you do need to clean it periodically. But there is absolutely no need to bake and sterilize anything. Even damp/wet soil is fine for them, as long as it's not muddy. Let them meet the microflora of the outdoor world they are soon going to live in. If you are feeding them medicated feed against coccidiosis (very good decision!), they actually do need to encounter the natural soil outside, with everything in it (even cocci) while they are still on the medicated feed. That's because their bodies need to learn to recognize cocci and fight it on their own. What the medication is doing is it weakens the bacteria, so that it's unable to make the chick sick, but the bacteria is still there for the chick's immune system to recognize it and learn to fight it.