1) Choose a crystal that you want to program. I enjoy healing with clear quartz and amethyst. A wand shape or a double terminated point is preferred. Use your intuition and choose a crystal that really feels right for the purpose.
2) Choose a location that is quiet and comfortable. It is important to be able to focus a loving intent when programming crystals.
3) Cleanse the crystal. Instructions on how to cleanse a crystal can be found
on this site or use a method that feels right for you.
4) Invite in your Reiki guides to help in the process.
5) Open the aura of the healing crystal by holding your hands, palms together as in prayer position, over the crystal. Separate your hands while turning your palms upward as if holding a book and place your hands down to the left and right of the crystal.
6) Using the first two fingers of your primary hand, draw the Reiki Master Symbol, Dai ko myo, over the crystal. Do not concern yourself about the size of the symbol, it does not have to “fit” on the crystal chosen. Simply draw the symbol over it and your Reiki guides will take care of the details.
7) Pick the crystal up and gently blow on it while visualizing the Reiki Master Symbol going into the crystal. Visualize the symbol glowing on the surface of the crystal and then sinking into it.
8) Place the crystal back down.
9) Draw the other Reiki symbols; Cho Ku Rei, Say He Ki, and Hon Sha Ze Sha Nen, over the crystal.
10) Pick the Reiki crystal up and gently blow on it while visualizing, one by one, the Reiki symbols glowing on the surface of the crystal and then sinking into it.
11) Channel Reiki healing energy into the crystal for 3-5 minutes. Follow your intuition. If you are guided to channel Reiki healing energy for a longer period of time, do so.
12) Place the crystal back down.
13) Cross your arms over your heart chakra and say, “Thank you, thank you, thank you” either out loud or to yourself. This is to express your gratitude to Spirit, your Reiki guides, and the crystal for facilitating healing in the world.
14) The crystal is now programmed as a Reiki Healing Crystal.
Crystals have good memories and the charge on your Reiki Healing Crystals are permanent until reprogrammed. If at any time you choose to change the program on the crystal, simply cleanse it and reprogram it for the new purpose. Some of the things you can do with Reiki Healing Crystals are included in the list below.
USES FOR REIKI CRYSTALS
*A TOOL FOR ENERGY HEALING SESSIONS*
*WEARING IT AS PENDANT FOR DAY-LONG HEALING*
*USE IN CRYSTAL GRIDS AND CRYSTAL LAYOUTS*
*RAISING THE VIBRATION OF YOUR HOME OR OFFICE
Exploration of the Sacred & Conscious; including Sexuality 
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very good informative article
Simple and straight forward. Please note that you need to be a Reiki practitioner to be able to program the crystal as instructed above.