You can open .mdr files by going into File>New... and then select Binary File. Click on Choose Elevation File and select your .mdr file you want to bring in (by default it filters for .bin files, so tell it to look for All Files). Don't worry about filling in all those parameters as Fractal Terrains automatically grabs them from the .mdr file. Then just hit Ok, Next, and then Finish.

There is an issue with .mdr files being flipped vertically in FT, but Wilbur does the same thing to .ftw files. You can either flip them before hand in Wilbur or afterwards in FT (Map>World Settings>Fractal Function and then check Flip Vertical).