Bash's cd command has a couple of interesting but little-used options, -P and -L.
   cd [-L|[-P [-e]] [-@]] [dir]
      ...    The  -P  option  causes  cd to use the physical directory
      structure by resolving symbolic links while traversing  dir  and
      before processing instances of .. in dir (see also the -P option
      to the set builtin command); the -L option forces symbolic links
      to  be followed by resolving the link after processing instances
      of .. in dir. ...
So ... if you're looking for the physical location in the filesystem of your current working directory, you could use something like this:
realwd="$(cd -P .; pwd)"
In your comments, you mentioned that you're looking for the parent directory of the directory containing a file -- so, if a path is /foo/bar/baz/filename, you'd be looking for /foo/bar.
To get this, I would suggest a combination of cd -P and parameter expansion. Since you know that the / character can never exist as part of a filename, the following might work for you:
grandparent() {
    local realdir="$(cd -P "${1%/*}"; pwd)"
    echo "${realdir%/*}"
}
This works by using cd -P to "get" the physical location of the file, then parameter expansion to strip off the last item in the path.
$ mkdir -p one/two/three
$ touch one/two/three/foo
$ ln -s one/two/three bar
$ ls -l bar
lrwxr-xr-x  1 ghoti  wheel  13 Nov 19 23:05 bar -> one/two/three
$ grandparent bar/foo
/usr/home/ghoti/tmp6/one/two