You can remove all Web access to a directory on your Windows hosting account by removing the "Anonymous Access" IIS Setting for that directory. The result of removing this permission is that you can only access that directory from with your hosting account or via FTP. You will not be able to access the directory through any Web browser, regardless of whether you are knowledgeable of the hosting account user name and password.
For additional information on IIS Settings, see What do the different IIS settings do?