First - I hope someone else can help you with the permissions settings, I see nothing in the Net::FTP module that allows for setting permissions.

Second, it would be helpful if you showed your code to see what you're doing so far. When deleting directories, which I have done via FTP as well, you want to start at the bottom, and work your way up the tree. If we saw your code, we may be able to point out how to repair this.

Thanks,