Set up the book shelves to create a space that is somewhat isolated from the rest of the room. You may wish to place a shelf perpendicular to a wall to create a "nook" for reading, or you can just place the shelves so that their ends meet in the corner of the room.
Place all the books on the shelves in an orderly manner. You should not have more than one copy of any book. Any oversized books that do not fit on the shelves should be placed on top of the shelves and bookends or a wall can be used to hold them upright.
Place the small table or desk and chair in the book corner. If you have already used a bookshelf to isolate the nook from the rest of the room, then you can place the desk so that it faces toward the shelves or away, depending on what your child prefers. While it is good for her to be able to focus, she should not become dependent on isolation for concentration. However, if you have placed the shelves all against the walls, you may want to position the desk so that a reader's back is to the room.
Make sure that the corner is well lit. Even if there is enough natural light, place a reading lamp in the area that can be switched on when the book corner is being used. This will insure that even at night there is no risk of eye strain.
Update your reading material regularly. Books that reflect a child's current interests and the topics being studied in school should always have a part in your book corner. You can never have too much material to choose from.