How to remove a book from iBooks
On a Mac, open the iBooks app.
Go to the iBooks Store (left of the toolbar, at the top).
On the right-hand-side, in the Quick Links list, click the Purchased link.
Books will appear; find the one you want to remove and hover your mouse over the cover.
A little 'x' will appear; click it to remove the book.


The book will no longer come up in iBooks (or any other locations), no matter whether you have set iBooks to show or hide iCloud items.