To form the use of "at" as a Place Particle, the 에 is missing 서. This would also be similar to "in", which would also be an acceptable answer I would think, since there is no other "in" being used within the remainder of the sentence. Is there another reason for the particle being half complete given this pedigree? My original answer was "There are only sixty-one books in the library."
The way I have been told 에 = location particle. 에서 = shows the location of an action. So if someone is doing something at the library such as 'I study at the library' 나는 도서관에서 공부해요. In this case, I don't think the 61 books are up to anything. The key I try to remember is if there is action involved.
The meaning is the same, but you'll probably need a different particle to make the library the subject rather than a location phrase. My guess is 도서관는 책 예순한 권만이 있습니다.
권만이 is the counter. 권 is a special counter for books specifically, and 만이 just means only, as in to describe the quantity.