Me, I always go to the Library, highlight the ebook in question and then press the Delete button on the left edge of the Cybook. That removes the ebook and it's two associated files.
Oh! Wait! That's in my fantasy dream! Yes, after more than one year of Cybook ownership - with the Delete button hanging out there on the left edge of each Cybook and Netronix EB-100 I own - I *STILL* cannot use this button to do what it was *designed* to do! (And it would be such a simple feature to add.)