Basically I want to know if I can remove them with a destroy target enchantment spell.
Nope, you cannot.
Cipher exiles the spell but is "encoded" onto the creature.
An encoded creature does not have an enchantment on it. It has a special relationship between itself and the exiled Cipher card. Destroying the creature can remove the encoded effect, as covered here:
702.97b The term "encoded" describes the relationship between the card with cipher while in the exile zone and the creature chosen when the spell represented by that card resolves.
702.97c The card with cipher remains encoded on the chosen creature as long as the card with cipher remains exiled and the creature remains on the battlefield. The card remains encoded on that object even if it changes controller or stops being a creature, as long as it remains on the battlefield.
RESOLVED
What Keyeto said...
So even if a card had protection from all colors it can be encoded? This is relevant to the {etched champion} discussion from afew hours ago
Quote from: MisterJH on February 06, 2013, 06:18:08 PM
So even if a card had protection from all colors it can be encoded? This is relevant to the {etched champion} discussion from afew hours ago
Encoding does not target or enchant, so protection will not stop it.
Thanks guys.