Hi Ironice, thanks for the file. One way that will work in the current MoI version is if you select the 2 spheres while they are separate objects without booleaning them together and then run the Fillet command.

That will do a surface/surface fillet instead of an edge based fillet and then use Edit > Join to glue the pieces together.

But I'll see if I can get the edge based fillet working too.

Thanks, - Michael