What follows is a simple purification ritual that can be used on crystals and stones, and other sacred objects. This rite is best done at sunrise or during the day, on your altar (if you have one) or on any table that can be used for this purpose.
Fill a basin with pure water and place this to the west on the table or altar. Next, light a red candle and set this to the south. Light some incense and place this to the east. Finally, place a dish or flowerpot filled with freshly dug earth to the north on the altar. In between all these objects, set the stone (or stones) to be purified.
When all is readied, still your mind and pick up the stone in your projective (dominant) hand. Turn your attention toward the bowl of earth. Place the stone on it and cover with fresh earth. Say something to the effect of:
I purify you with earth!
Leave the stone there for a few minutes, all the while visualizing the earth absorbing the stone's impurities. Then remove it, dust it clean, and hold it in the incense smoke. Pass it nine times through the smoke, from the right to the left, saying words like these:
I purify you with air!
Next, quickly pass the stone through the candle's flame several times, saying:
I purify you with fire!
The fire burns away all negativity. Now place the stone in the water and say this or your own words:
I purify you with water!
Visualize the water washing it clean. Leave the stone in the water for a time, then dry it with a clean cloth and hold it in your receptive hand. Is the stone "clean"? If not, repeat this simple ritual as many times as necessary, until your are sure it has done it's work. Afterward, store the stone in a special place. It is ready for use in magick.
From: Cunningham's Encyclopedia of Crystal, Gem and Metal Magic