Many users will have hundreds or thousands of bookmarks. Note Firefox's bookmarks library may use nested folders.

If you import HTML favourites they get appended to the end of your bookmarks, possibly in a folder. You may mark select multiple bookmarks or even folders and delete or copy them. You may find it best just to put the old bookmarks in a folder in case you need them. If you are deleting most of them maybe it is easiest just to select those bookmarks you want using Ctrl + Left Click and copy those to a folder and then delete the remainder. Note Ctrl+A will select all the bookmarks in a pane including those scrolled off the screen. Just one warning sometimes firefox may be rather slow in doing big tasks on the bookmarks.

• Use bookmark folders to organize your bookmarks

You may find it wise to make backups of the.json type whilst you work with your bookmarks so that you can go back if something goes wrong. CARE take note .json type restores overwrite your existing bookmarks. (.json tyoe have more features: tags, keywords, and a folder structure)

• Import Bookmarks from an HTML file
• Restore bookmarks from backup or move them to another computer

Note also it is possible to automatically sync bookmarks between devices.

• How do I choose what information to sync on Firefox?

You can delete the places.sqlite file to reset the bookmarks and the history.

• http://kb.mozillazine.org/Profile_folder_-_Firefox

• http://kb.mozillazine.org/Backing_up_and_restoring_bookmarks_-_Firefox

JNA Penna reply: I found this solution by john99 most effective: the responder is quite right that Firefox was very slow to delete large numbers of bookmarks (I had hundreds)- I would keep getting to NOT Responding even if I used Control A to delete a group (20) of bookmarks- so what I found most effective was to simply delete them one at a time with the delete key. That way when it would stall at a big folder, I waited for it to disappear than zip through others that went right away.

     Then I imported the html file with the best set of bookmarks which I wanted to use and from the backup folder that I created before deletions, I selected those that were not in my new file and placed them in the new bookmark files.
     Many thanks

Glad it worked.

cor-els's solution would have been quicker in clearing your bookmarks but has the big disadvantage that it would have deleted all History and all bookmarks, and I thought you may have wanted to keep some of the existing ones.
Thanks for posting back.