Once you have cleansed and charged your crystal, you can program it by setting a specific personal intention for it.
First, you need to do your own research and pick a crystal that resonates with your intentions, desires, and goals. Some crystals like Quartz are already naturally programmed; you just need to match your intentions with the right crystal.
When choosing your perfect crystal, try to listen to your intuition rather than your rational mind. It will seldom steer you wrong.
Programming is ideal when you need to be very specific about using a particular crystal. You will want to carry the crystal with you for a long time, wear it as crystal healing jewelry, or use it in creating a crystal grid.
It is not necessary to program your crystal when you will only be using it for a few minutes or a day at the most. If you want to benefit from the metaphysical healing properties of your crystals, or if you have chosen them based on your instincts, there is also no need to program them. However, you should also keep in mind that your intentions and desires should follow the crystal’s natural properties.
When you program your crystal, you are sharing your thoughts and emotions about anything that you need help with. A good idea is to write your intention down on a piece of paper that you can refer to anytime.
Some examples of intentions may be more openhearted in my relationships, be more patient, stay grounded and protected, etc.

Setting your intention.
Start with holding the crystal in your dominant hand or close to your heart. Quiet and clear your mind of any negative or unwanted thoughts, take your time, this will get easier with practice.
Focus on your crystal and the intention you have chosen for it, describe your intention aloud, and repeat these words until you feel this energy has connected with your crystal. Your intuition will tell you when your intention is set. You can also visualize yourself actually living your intention. This helps to boost the intention.
Revisit the energy.
Keep your crystal in your pocket, on your desk, under your pillow, or next to your bed to serve as a constant reminder of the positive intentions you have set. Revisit and reset your intentions weekly to continue on your positive journey. Stay conscious of the energy you are bringing in. Be positive, and positivity will come to you.