Wrap each stone that's to be cleaned in a cloth, and bury it in an undisturbed place for a period of time, preferably 3, 9 or 13 hours, days, weeks or months. The longer the period of time, the better the cleaning.
Other ways include placing the stones in a bowl of salt, free running water, suspending in a fire, or under a fire, or just suspended so that nothing is touching them. Any of the elements can be used; leave it in sunlight, rain, or any place you'd feel comfortable.