This document explains how to delete bookmarks in Safari that is running on Mac OS 10.10, but the same method can be applied for 10.9.
- Open Safari. On the top menu click on Bookmarks. Then click on Edit Bookmarks.
- The bookmark list appears. Select any bookmarks or collections you want to remove and right click (Ctrl-Click if your mouse only has one button) and select Delete. If you change your mind, choose Edit > Undo Remove Bookmark.
- Go ahead and navigate to a new page to close the Bookmarks menu window.
You can quickly delete links from the favorite bar by right clicking and then clicking Delete.
The Bookmarks bar and Bookmarks menu can't be deleted.
Address Book / Contacts (if present) and Bonjour can't be deleted, but you can remove them from the list by unselecting them in Bookmark preferences (found by opening the Safari menu and selecting Preferences... > Bookmarks).
History and All RSS Feeds can't be deleted, but you can delete individual bookmarks within them.