Please advise

I recentley recovered all the data I require, but the file folder structure is not correct.

I see that there is an option to enable this before you start the recovery process, is there any thing I can do at the moment without making it worse? I really need to directory structure.

in all honesty, other than re-recovering everything with structure enabled and using what you've already recovered to replace like files which failed, not much. That said you should just be glad you recovered the files and put them "away" manually.