There are many ways to cleanse or clear crystals and you may like to try out several methods to find the way that feels most effective to you. Some Teachers notably Serge King do not think clearing stones is ever needed.
I find that clearing stones can be a big help sometimes as everything does pick up energy impressions and when used actively crystals can soak up a lot of pain energy etc.
When using energy and intention based methods to clear your stones you can program the crystal to retain or restore its ideal state and or previous programming and memories rather than totally erasing them. Consult the crystal intuitivly for a sense of how much it needs to be cleared .
Drastic Methods Salt Water Earth & fire
The most commonly used clearing method of soaking them in sea salt water is no longer recommended for general use because it is rather drastic and can harm many kinds of crystals both physically and energetically. You can save that for really heavy duty cases.
In some cases you may want to keep the negative energy of a stone that has a important message and only shield it from accidental activation (I am thinking of someone's small stone that was picked up at Dachau).
Another drastic method is to bury your crystals in Earth Stones that you feel are extremely negative can be buried in earth for an entire moon cycle. or longer . you will need a sure way to find them . placing stones in fire is not reccomended by me as it may damage or destroy many crystals.
Please remember that it is common for the mind to amplify the energy received, and sometimes high vibration positive energies can feel prickly and uncomfortable if you are not ready for them.Some people tend to refuse to recognize that stones have been cleared to the point of returning undesirable energies to the cleared stone with their own mental intention.
Dry Salt & Vinegar
Leaving the crystals in dry sea salt overnight or longer is another somewhat heavy duty clearing method. Soaking the crystals in a solution of 1 quart of warm water with one tablespoon of sea salt and a quarter cup of apple cider vinegar for 20 minutes to half an hour is a quick clear technique that is not as drastic and seems quite thorough .
Salt can be harsh and many stones are water soluble or other wise potentially harmed by water. some of these these include Halite (salt), Sylvite, Desert Rose Selenite, all Selenite, gypsum angelite , Azurite ,Talc. calcite may dissolve in water as may Alabaster ,Sulfur dissolves in salt water. I have been told that any stone that has a name ending in ite can probably be damage by water though I am not sure of that.
You can also smudge your crystals with sage, sweet grass, cedar ,sandalwood or other clearing smoke or incense ,fanning the smoke over them or holding them in the smoke make sure that all sides of the stones are placed in the smoke. This works well and can be used on delicate crystals that can not be placed in water or salt without damaging them.
Clearing With Crystals
Small crystals can be cleared by leaving them on a large crystal cluster, either clear Quartz or ameythst . I have heard of using a selenite wand this way but have not done it myself.
Breath techniques are very effective for small pieces, hold the stone to be cleared in your dominant hand (the one you use to write with) take a deep breath in through your nose and focusing your intention on clearing the stone expel your breath firmly onto the stone from your nose , repeat until you have covered all sides of the stone either a long slow exhalation or short quick bursts are effective choose the way you prefer. you may also take a deep breath through your nose and holding the stone in either hand with your mouth slightly open expel your breath through your mouth slowly over the stone while making the "ha" sound .
Using energy is very effective ,Reiki, Huna, Rainbow Light , crystal clearing shakti, of course, Most general purpose healing energies and universal chi etc. work quite well if you are attuned to them or have practiced with those that come in without attunements .
Generally just run the energy into the stone until you feel that it is cleared. Crystal clearing shakti if you have it, is autonomous and once you have started it running on a stone or group of stones it will work until done without further attention or intention on your part. Holding the piece between both hands while running energy or beaming a flood of spiritual light into it also works. With most intelligent energies you can add the intention that the crystal become self clearing.
Some energy is also very good for charging stones to amplify their natural abilities Using direct intention can be very effective if you are able to focus your intention and are not over doubtful of its ability to clear crystals ,hold the stone in your hand or palm or place your hands on or over it and focus your intention on clearing it, for most stones a minute should be long enough to clear it.
If you are skilled at remote work or have an aptitude for it you need not actually touch the stone. Intention is also used to place a shield around a stone that you wish not to clear but only prevent from broadcasting generally, The "Never Again" stones from Dachau etc. being prime examples as these can be used to promote recognition of the truth and compassion.
Light & Sound
Colored light either from actual light or energetically is also used white ,gold, violet and blue being commonly but not exclusively used . Toning , bell ringing, chanting and other clearing with sound can also be effective and enjoyable Aum, AH El EE Oh, Ha , being only a minute fraction of sounds that work for clearing playing healing music and drumming work.
Sun & Moon
Placing stones in Sunlight or Moonlight is also good for clearing and charging them .Some stones are faded or otherwise distressed by direct sunlight. This may include Amethyst, rose Quartz, Citrine, Celestite (particularly blue), Aquamarine, Moonstone and Fluorite. Some turquoise may fade. A chunk of blue calcite faded after a while and I have also heard hat Realgar and pyrope can dissolve in air rather than sunlight. Stones are left in bright sunlight usualy from 3 hours to all day but strong sunlight may take as little a 30 minutes or even less .
Running water works well for clearing stones that are not harmed by water . A spring or stream or the ocean waves is best though you must be careful not to lose your stones to the ocean or river. Holding crystals under the tap will do in an emergency . Some people like to leave theirstones out during rainstorms too. Many people also bathe with their crystals which not only clears and charges the stones it is very refreshing and healing for the bather as well.
Gentler and slower methods include immersing the stones in rose petals or lavender petals or sage, thyme or Rosemary leaves or in feathers or charged sand just putting the stone on a sacred altar or in a place with healing energies will also work over time.
Caution When Using Running Water
Running water works well for clearing stones that are not harmed by water.A spring or stream or the ocean waves is best though you must be careful not to lose your stones to the ocean or river.
Holding crystals under the tap will do in an emergency . Some people like to leave their stones out during rainstorms too. Many people also bathe with their waterproof crystals which not only clears and charges the stones it is very refreshing and healing for the bather as well.
There are angels and Deva and other spiritual beings who can and will clear crystals when you ask them learning to connect with your high self and Companion Angel will help you learn to work with the stone people in a depper way.
Most of what determines whether these methods work for you is your belief system and your intention . Any of these methods will work it is up to you to find those that feel most effective to you.
Many of the techniques for clearing crystals also charge and restore them but sometimes A crystal that has been cleared seems under energized or even lifeless. It can be charged ,amplified or restored by several methods.
First I usually hold the stone and intend that it natural energies be amplified using a scale of one to ten . There are attunements that can facilitate this and other energywork and crystal work processes .
I find that many people can access these procedures quite well without formal attunements. It takes less than a minute for most of these intention techniques to work and most will run to completion by themselves if you do not retain focus on the stone. Simply intend that the stone's energy be raised to its highest most healthful level ,or restored to its ideal state.
You can also use intention to personalize a stone for your self or others this will call in harmonious energies and turn off inharmonious ones. You can also use intention to recover programming or memories that have been cleared out previously if you need too.
In most cases if you have a piece of the same stone that is fully energized you can place the under charged stone next to or on it and ask intend that the weak stone match it and restored to the full level of its potential.
You can ask your Solar Angel and high self to charge and restore a stone or bring in the Guide or Deva most suitable. to do this.
Sunlight, moonlight, wind and other Spiritual intervention will raise the vibration and restore wholeness to your stone's energy. If you run crystal shaktis or stone spirit energies you can charge your stone simply by running the stone shakti of that stone into it .
It is possible to program your crystal or other stone to hold a message , work for a specific purpose, broadcast an affirmation, or emotion , enhance protective filters , communication, meditation and healing work and an almost infinite number of other purposes. Before we had computers we called this process "enchanting".
I strongly reccomend programming a single terminated quartz crystal to help facilitate your connection and awareness of your high self and/or companion Angel and carrying with you in a pocket as often as you can.
If you do not have a particular stone or crystal that you need for a particular purpose you can use a quartz crystal and ask/intend that it be charged to act as the needed stone ,Make sure that you clear it when you are done using it as an energetic substitute.
Quartz crystal is most often used for programming, though most stones can be used. .Keep your programs in harmony with the natural energies and purpose of the stone . Singly terminated quartz crystals are most often used though round crystals and stones are very good also.
It is quite important when programming a crystal by intention that you are quite clear and focused on just what it is that you do intend. You might want to write down your proposed program first and before you program a stone or other object to promote a particular emotion think it through carefully.
I once charged a stone with the intention that it promote happiness in a large room and after a few days we all became very irritated at the constant "Happy" energetic nagging . It was just not comfortable or natural.
I also once programmed a stone to promote sleep in a bedroom and it was so effective that it was virtually impossible to do anything else at all in the room until the stone was cleared. My Love life virtually disappeared. It even had a plumber and a heater repairman struggling to remain awake to their great puzzlement.
Programming for mental alertness and emotional clarity has not caused any difficulties so far. You want to help not overpower these cautions apply even more strongly to programs for Love etc. if in doubt don't do it!. Crystal programming is to be used only for good and in accord with Your soul purpose . You cannot and should not use these techniques to try to manipulate others .
First and foremost clarify your intention, hold the stone in your dominant hand or in both hands. Large stones can be touched rather than held. Focus your intention on the stone. Clearly state in your mind or out loud what it is you are programming the stone for. Visualize the desired result as clearly as you can if appropriate.
To program a stone to broadcast an intention ,prayer ,desire or affirmation or healing energy you just intend that it do so . One to five minutes is the standard time to hold the focus. You can intend that it activate only when you hold it or when you call on it rather than having it be contstantly active depending on the purpose you are programing or dedicating it too.
You will probably find it most effective to hold the stone in your non dominant hand to receive and your dominant hand to program or to amplify sending of healing energy .
Some crystals have already got a firmly set memory and purpose , these are not appropriate to use for you own programs . You should have an intuitive sense that it is suitable to program the stone for what you intend before you do so.