Here are the principle methods:
Bury the gemstones in the Earth.
Wash the gemstones in running water.
Bathe the gemstone in sunlight.
Pray to higher beings, God/your higher self to cleanse and purify the gemstone.
Visualize the gemstone surrounded by purifying white light.
Place the gemstone near gemstones that transmute negative energies to positive etc.
Suround the gemstone with herbs that have the metaphysical property of purification.
Ask an advanced incarnate being to purify the gemstone for you.
Dedicate the gemstone to the highest good for all beings.
Love the gemstone unconditionally and warmly.
In the ideal database of theraputic gemstone properties there should be a note with each gemstone regarding it's purification needs.