First make sure you do a Tools, Check on the geometry, with validation turned on. Next, I would run an import diagnosis, and ask it to improve the geometry. You can also use import diagnosis to remove faces, but I would do that with the feature based tools, because diagnosis leaves no history of what you did or way to undo it other than reimport.
Are you having problems deleting the faces or closing the gaps? Have you tried to delete all the faces of the fillet and let SW close the gaps on the solid (without leaving it a surface model) automatically?
formatting link
If you have to do this manually, the section where the smaller fillet runs into the flat face (blue arrow) will need to be trimmed square before it will knit solid. That combined with the fact that the edge that feathers into the smaller fillet (red arrow) is likely to create some very nasty small edges will give you some challenges. You may need to construct a new surface in this area instead of trying to extend the green arrow face. The new surface will need to be an extension of the face indicated by the black arrow, or it may be easier to delete the black arrow face and just recreate it altogether, and trim it with the flat face with the hole on it.
The larger fillet looks fairly easy from this distance.
If you get really desparate, email the part. It may take some swearing, but I think this can be done.
matt