Stones, especially those which are bought, are subjected to a wide array of energies before they even reach your home. For this reason, many magicians cleanse and purify their stones before using them in magic.
It's a fairly simple process which removes negative or distracting vibrations which the stone may have picked up from past owners and handlers. The only exceptions are those which you have collected, unless they were near a military institution, highway, or polluted ground.
There are several methods of doing this. The simplest is to place them in full sunlight for one, three, or seven days, and let the Sun do the work of releasing any negative vibrations from them. Remove the stones each day at dusk.
The second technique is a little harder, or if not harder then risky at any rate. Put the stones in a net bag or devise another means of securing them, then place the bag in a river or stream, tying one end to something secure enough to keep them from washing away in the current. This method uses the element of water to gently wash away impurities.
A third technique utilizes the element of Earth. Bury the stone or stones in the earth uncovered, and mark the spot where you laid them. Come back in a week and they should be completely purified and ready for use in your spells or meditations. If not, bury them again.
These are all natural methods of cleansing and purifying your stones and should most likely be used before extensive rituals and spell-casting. I prefer sunlight or burial myself.