There are two ways to remove runes from equipment:

1. By crushing the rune. You will free up an equipment slot, but the rune will be destroyed. 
2. By applying the Runic Knife item. In this case, a rune is saved in the Collection and may be used again. To remove a rune of a specific class, you need a Runic Knife of the same class or higher. The Runic Knife is destroyed after use. You can purchase it in the Bonuses section of the Item Store.