I dip them in a diluted solution of bleach, potasium permanganate, or some other cleaning agent (ammonia maybe?). Usually just put them in a bucket of water with a splash of bleach for a day or so. My method may not be perfect -- do a search on bleach dip or potassium permanganate and you'll get more info.
And be careful with the potassium permanganate, I'm told it's violently reactive with formalin (common fish med). I don't really know what kind of reaction, and now I'm actually super-curious. dang.
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