Intention is the simplest, most effective, and least costly way to clear and charge a crystal. To begin, roll the crystal in a clockwise direction with your predominant hand, pressing firmly on each of the crystal's facets. This creates a piezoelectric charge. (Piezoelectricity is simply the ability of some materials, including certain types of crystals, to have electrical properties under stress.)
Next, press the forefinger of your predominant hand onto the tip of the crystal and place the forefinger and thumb on your other hand on the sides of the crystal to create a cross current. Next, focus all of your attention on the stone and mentally transfer your intention to clear the stone into the stone itself. Think a thought to yourself along these lines: My intention is to clear this crystal, releasing whatever is not for my highest good and for the highest good of all concerned. Then, complete the process with a confident, forceful breath through your nose (a pulsed breath). The force of the exhaled breath is similar to the force of a breath you would use to extinguish a candle.
Repeat this process for each pair of facets on the crystal. For example, a quartz is a six-sided gemstone, so you need to repeat this process three times because you're holding on to two sides at a time. In the case of tumbled stones, larger crystals, or a large assortment of crystals, it isn’t necessary to hold the crystal or the group of crystals in your hand to clear them. Simply look at each stone you want to clear and make the strong intention that it will be cleared. Follow this with a pulsed breath.
Breath and intention as well as mental focus and transference of thoughts and visualization performed remotely are effective as well. You can clear your house, your office, or car in the same manner. The plan is to hold the intention and visualize and know it is effective.
Other ways to clear your crystals include smudging with herbs and resins, salt baths, running them under tap water, holding them tightly in the ocean as the water cleanses them, and placing them for a time in the sunlight or moonlight. If you choose to use salt baths to clear your crystals, quickly pass them through the saltwater, then rinse and dry. Many polished stones will lose their shine after sitting in saltwater. This goes for the ocean as well. Be sure to hold on to your stones at the beach very tightly. Many a stone has returned to Mother Earth this way.
From The Essential Guide to Crystals, Minerals and Stones, by Margaret Ann Lembo