How can I remove a Darksteel Citadel animated by Nissa, Worldwaker?
Any card that says "Exile target creature", "Exile target artifact", or "Exile target permanent" will remove an animated Darksteel Citadel. Cards that do this include


Devouring Light
Pillar of Light
Ashen Rider
Chained to the Rocks
Curse of the Swine
Excoriate
Fade Into Antiquity
Gild


In addition, if it's toughness ever drops to 0, it will die as a state based effect. Lash of the Whip, for example, will kill it.