What kind of rune is it? To use it, double-click it then click on a piece of your armor.
Some thing to know about runes:
-You can only use runes for your main build, i.e. warriors use warrior runes
-A few runes, like Vigor Runes, can be used by everyone
-Runes don't stack. You can only use one type of rune at a time.
You can only have one rune per piece of armor. If you try applying a rune to a piece of armor that has a rune, then the second rune will override the first.
You can only have one rune of each type. That means that a Monk can either have a Major rune of Healing Prayers or a Minor rune of Healing Prayers, but not both.
Minor runes add +1 to a single attribute. Majors add +2. Superiors add +3. Minor Vigors add +30 health. Majors add +40. Superiors add +50. I believe that Minor Absorptions add -1 damage reduction, while Majors add -2, and Superiors add -3, but I'm not sure.