For example just looking at only all the wire curves and not any surfaces it is hard for me to figure out which particular area you were trying to fillet in the 3DM file...

One thing that could be an issue for filleting is that things to fillet should actually come to a sharp corner, if you've got things already nearly smooth that can be bad for filleting - it can be better for filleting for the pieces to be more like separate parts that intersected one another rather than trying to do an edge-to-edge skin that has surfaces that meet each other in a shallow angle being somewhat close to smooth already.

- Michael