。
Put the books back where they were.
Literal
Books [topic-は] originally was place [at-に] return-[prepare-ておく]-[gentle-imperative-なさい].
A relative clause もとあった場所 ('the place where (it) originally was'): もと ('originally, formerly') + あった ('existed') modifying 場所 ('place'). 戻す ('return, put back') + ~ておく ('do in preparation / leave in state') + ~なさい (gentle imperative). The preparatory ~ておく here means 'put back and leave it there.'