This worked like a charm… almost!
Due to a bug in iCloud a while back, I ended up with thousands and thousands of duplicate bookmarks. This started to cause issues in El Capitan (which is also buggy in a number of places) because iCloud was having issues syncing all of these. I installed this app and bam… all of those iritating bookmarks were removed. Awesome! However, I need this tool to also remove empty bookmark folders. Now I have about 10,000 empty folders. If this tool did that… five stars!
Peanut ATC about BookmarkApp