Sounds like you just need to organize your bookmarks now.
Goto the URL opera://bookmarks.
Under "other bookmarks" in the left-hand pane, click a folder that has "imported" in its name. The bookmarks and folders for that imported folder will show in the right-hand pane. In the right-hand pane, select all bookmarks and folders by left-clicking in a blank spot below the horizontal line on the page and hitting ctrl + a. Then, drag the selection to "other bookmarks" in the left-hand pane to move all of them out of the imported folder.
Repeat that with other folders with "imported" in their names. Then, when you're done, all the "imported" folders will be empty where you can right-click them and move them to the trash. You can then right-click the trash and empty it.
For any "Bookmarks bar" folders that were created on import, drag their contents to the main "bookmarks bar" folder in the left-hand pane to move them out of the imported folders. Then, you can move all those empty folders to the trash again.
Also, in the right-hand pane, you have the option to edit the names of any folders you want.
Also, if there are any folders that contain all duplicates, you can just move the folder to the trash.