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...