Crystals are formed by a vcry slow and controlled heat reduction process. Chemicals used during the process, as opposed to dyes, dictate the color. Different chemicals absorb different wavelengths of visible light. The result? We see the opposite of this color.

For example, if the chemical added absorbed blue, we would see an orange crystal.

Interestingly enough, manufacturing a clear crystal is much more difficult than adding color. There can be no impurities during the manufacturing process as even a small contamination could change the clarity of the crystal.