You can, if you wish, just right click any link from your bookmark lists and select "delete" from the drop-down menu. But as green granite has suggested it's better to completely re-organise things via the "Organise Bookmarks" option. You can move them up and down by drag & drop with this function to get them in the order you want.
There is a handy little "Add on" called "Moz Backup" from the Mozilla site which will make a complete backup of your book marks, and also your Email contacts. Handy if you ever have to reinstall.