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
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