yEd does not provide an output option that specifically and only yields the coordinates of the nodes. The standard GraphML file representation of a diagram contains the coordinates, of course, and you could obtain them from there.
If the question is actually regarding one of the yFiles programming libraries, please contact yWorks support by email to learn about the available options with the specific library. (Please include your yWorks customer ID or evaluator ID in your email when doing so.)
Note that this forum is for yEd questions only.
