"Denaturing" means to make the protein take on a different shape, which is all that is necessary (since a prion is the correct amino acids arranged in a pathological arrangement). You can denature proteins with heat or very high or low pH, depending on which protein that it is.

But the dangerous part of a prion is the way it's folded, right? All you have to do is denature it to render it harmless. It's just harder to do for some proteins than others.