The ".MDF" extension stands for "Mapper Data File". The MDF file contains information about how gates that were implemented using more than one LUT are composed. This information is used as a "hint" to MAP when MAP is run with the guide (-gf) option.
For 4-input gates, MDF data is generated only if more than one LUT is used to implement the gate. If MAP implements the gate in a single 4-input LUT, the decomposition information is not needed, so it is not generated.
For example, suppose you have a 5-input AND gate. Depending on how this 5-input function was implemented, the MDF file could indicate that the logic function was separated into a combination of a 3-input F-LUT and a 3-input H-LUT, or a combination of a 4-input F-LUT and 2-input H-LUT.
When you specify the "-gf" option or use the browse button in Design Manager, MAP will pick up the .mdf by name association. (The MDF file name is implied by the guided NCD name.)
For example, if you use "fred.ncd" as the guide file, the mapper looks for a file (in the same directory) called "fred.mdf". However, in Design Manager, the .ncd file is called "map.ncd", so the .mdf file should be called "map.mdf".