First, I turn off bookmark sync on all of my devices (MacPro, MacBook Pro, 2 iPads and an iPod touch). The iOS devices ask if I want to delete bookmarks and I say "tes."
Second, I start deleting all of the many, many dupes and unwanted bookmarks. After great effort, I am satisfied with the result.
Third, I turn bookmark syncing back on for my MacPro. That's when the deleted bookmarks start returning. It's veritable whac-a-mole game but it isn't much fun at all.
I need to clean up my act but iCloud won't let me do it.
Delete the bookmarks you don't want from one of your devices while you are still syncing bookmarks on all your devices. The bookmarks will be deleted from iCloud and your synced devices as you delete them (although their may be a bit of a time lag).
Retrieving data ...