Apple re-engineered iBooks in Mavericks, but it’s a little under-implemented. One omission is that you can’t delete from iBooks books and PDFs you manually added into iBooks itself. I’m assuming Apple will fix this, but for now I have a workaround which involves creating a special collection called Trash. Into Trash I then put the books I want to delete, close iBooks and run a script to empty the Trash collection.

The script first finds the sqlite3 database containing the iBooks data. This at the moment will be beneath:

~/Library/Containers/com.apple.iBooksX/Data/Documents/BKLibrary

Next we look in the ZBKCOLLECTION table to find the Trash collection, and get its ZCOLLECTIONID.

If we do find that we need to move to the ZBKLIBRARYASSET table and find the paths ZPATH and titles ZTITLE for the books in the Trash collection. We ignore books with a purchase date (ZPURCHASEDATE is null).

Finally we rm -r each such path. Reopen iBooks and it will realise the files have gone missing, and forget about the deleted books.

This only works for books that have been manually added, not for books bought from iTunes for instance. Those can and should be deleted just inside iBooks itself.