Can't delete folder on Western Digital External HDD

I use the program there came with the disk, WDSmartWare. It's OK, but i can't delete the backup. It sounds strange to delete a backup, but it's because it's an old backup from another computer.

I've tried to delete the folder in Ubuntu which i've installed on a third-partition. It seems to work, but when i change to Windows there is a folder named .Trash-1000. I HAVE emptied the trash can in Ubuntu. If I rename the folder in Windows to f.x. "Delete me!", I can see it again in Ubuntu. Maybe I have to say that i've a bit problems when i have to remove the HDD from Ubuntu. It's says that there still is a process running, but the process doesn't stop. I've waited for an hour now. If I right click on the process and select "End task", Ubuntu works a few seconds and when it says "You can remove the movable disk now".

I've also tried to delete the folder in Super-admin account in Windows.

What can I do more?

Sorry for my bad english!

Uninstall what? WDSmartWare? But it aren't installed in Ubuntu, so I can't see what it'd help.