well, from putty I'd think you'd just go ahead and delte the directory if you can. To accomplish this, the first thing to do will be to 'move' into the parent directory of the folder you want to delete. to do this you'll use the "cd" command. (the directory structure here is the same as ftp) First, move into your domain.com direcoty - tyep:
actauly, after you've typed the first few letter of the directory you can press tab and it should auto complete for you. If the directory you want to delete is directly under the domain.com folder, then we can move onto deleteing, if not, move into the appropiate direcoty.
You can see the files and folders in your current directory by typing "ls" - that will list all of the files.
Once you're in the right place, it's time to delete that annoying directory. Be sure not to delete the wrong thing here, theres no recycle bin. you'll use the "rm" command, but with a few options. If the direcotry you want to delete is called mt, then you'd type:
rm -rf mt
That will hopefully clear out the directory for you.