It's pretty simple. In order to delete books from your bookshelves you simply have to select them using the dedicated button on the top right corner of the screen and then you hit delete. If you still see the book icon (with a cloud on one of its corners), then you are deleting a purchased book, that is available always on the cloud. To make the icon disappear you can either hide that book from your purchases or decide to not show your iCloud books on the shelves (from the list of your collections).