Smudging is the term for brushing or smudging away unwanted, negative energy using sacred or scented smoke. Crystal and gem stone jewelry can be smudged in the same way to clear their energies, also.
To smudge a crystal, prepare by bringing choosing your sacred smudging materials and bringing them to a safe place to use flame.
Carefully light your smudging materials and fan them gently with your hand or a feather to smolder and give off smoke. Say a small prayer or ask the Divine to help clear the energy of the crystals to be smudged for the highest good of all concerned. Then slowly pass the crystal through the smoke three or seven times, or brush the smoke over the crystal the same number of times. Do this for each crystal you wish to smudge clear of unwanted energies.