In the process of Clearing the crystal - it might be a case of clearing out previous programs, before clearing make yourself aware of the type of crystal that you are going to be working with, know the basic type of crystal, is it a generator, channeling etc. it is better to know the energy  that the crystal is, its a matter of the right crystal for the right work, ( there are many books available which describe crystal forms).
Warm the crystal by rotating it in your hand, when  it is warm put your thumb on the crystal face (there can be as many programs as there are faces). With the thought of clearing blow a quick short breath onto the face, clearing it out.
To program do the same as clearing as far as warming the crystal and holding the face with the thumb and place a thought into the crystal, ie. "I dedicate you to the healing power of the universe" or if you know the specific formation, you can dedicate it to release the power and force of its nature. Then you blow into it with a long breath.