Cleansing should be done on a regular basis in order to clear old thoughts and intentions to make room for further expansion. You can cleanse by sage smudging the crystal by engulfing it with purifying smoke, run through a fresh river or spring water, or use a piece of selenite to absorb the unwanted entities within the crystals.
Gather a bundle of dried herbs, light on fire, and use the smoke to purify and remove any kinds of toxic energies
Run through fresh natural spring water or the cleanest ocean water for best results. Make sure the crystal/stone isn't going to disintegrate or be damaged by being exposed to excess moisture. I reckon it wouldn't bring harm if you lightly sprinkled the water as opposed to engulfing the entire object.