To get rid of the Bookmarks and Bookmarks Folders you don't want, just drag them off the bar, just like you do with unwanted Dock icons. (See this tip.)
Use care, however. If you drag a Bookmarks Folder off the Bookmarks Bar, all of the Bookmarks in that folder are deleted.
If you want to remove a specific Bookmark from a Bookmarks Folder on the Bookmarks Bar, a couple of extra steps are necessary:
- Click the book icon at the very left of the Bookmarks Bar. This will open your Bookmarks organizer.
- Make sure that Bookmarks Bar is selected under the COLLECTIONS header of the left pane. This will show all the Bookmarks of your Bookmarks Bar.
- Open the folder you want to change by double clicking on it.
- Select the bookmark you want to remove and press the Delete Key.