When you are in iBooks and looking at your bookshelf, tap the "Edit" button on the top right side. Then, press the empty circle that appears next to each book you want to delete (you'll get a blue circled check). Then, hit the red "delete" key at the top left side and, all the books you selected will be gone.
If you accidentally hit the 'delete this copy" button in the pop-up that shows up, the book will appear to stay on the shelf but it will show the cloud-like download button next to it. To actually remove it from the book shelf, you have to press the red "Delete" button in the pop-up. Then it will disappear from the bookshelf (you can still get it free on a -download from the store).
Note that this is if you are in Books in your Collections. If you have enabled your purchases to show in the bookshelf and you are in the "Purchased Books" section of your iBooks app, then the books will not be deleted and will appear to be in the bookshelf. For that, just change your Collections view to Books (or a category that you've made).
Now, if you don't want the Purchased Books to appear on your iBooks bookshelf at all, go to the iBooks tab in your Settings app, find the line 'Show All Purchases" (on the right side) and turn it OFF. Then, the books won't show until/unless you actually go to the Apple Store.
Whew! That was probably way more than you needed. But - hopefully some of it was helpful.
Marilyn