Well.. well..
Do you need to display window that interacts to user. And you need to control that from your Fortran program? Why is that?

If you just need MFC and to display some GUI, you can just use dialog (CDialog), and display controls in it. Write code to control window in CDialog's derived class.

But if you must display entire window (SDI), I would recommend you keep the MFC project as exe only. Further to that, implement some IPC to communicate from Fortran-process to MFC-process. Choosing IPC mechanism, out of mutex, pipes, mailslots, sockets, clipboard... all depends on your requirement.

SQL Server is an example. It displays everything with client process, but performs database operations in non-GUI service (sqlserver.exe).