Mount points are empty directories. In Linux, all filesystem is mounted in one tree, and Ubuntu is a Linux. You tried to remove that directory using
rmdir command. It's OK. But it said permission denied. It is expected to happen. You are not the owner of neither those directories nor the parent directory,
/mnt . You must have superuser permissions to remove those. So use
sudo which give root permissions like this:
sudo rmdir /unused/mount/point/
It will prompt for the password. Type your password and hit enter. Your password won't be seen, even not dots. That's normal.