Re: Cube with Rounded Corners

instead of Fillet use Bevel which does the same thing only on just the edges you select. So if the cube is editable, use Edge mode and select only the corners you want to round, make the Type Convex and set the Subdivisions to "high enough to get it smooth enough for your needs" and check off Create N-gons so you get a top surface you can run an Inner Extrude on.

or

the extrude should work if Caps are turned on and the spline you are extruding is Closed.