To open or save a structure:

• Click on the Open Structure  or Save Structure  button in the Structure Editor window.
  
  
• Choose the File | Open | Structure or the File | Save | Structure menu item.

If you are opening a file which contains more then one structure (*.sdf file), only the first structure in the file will be loaded into Structure editor.

Mass Frontier is a 32-bit application, so you can use long names to save structures. You can even save structures by their actual names (e.g. 1-Amino-2-hydroxyindane.mol).