You can use direct editing on many Rhino geometries by holding control + shift and simultaneously clicking on a surface for example. Or select one surface after another, while holding control + shift
Use the gumball to scale with factor 0 to make it flat.
Use the gumball to move your geometry or parts of it to a certain height
Not sure if your bottom surface needs the division. You can get rid of it with the command MergeAllCoplanarFaces
If instead you just want a clean surface instead of the many isocurves, you can delete it and type cap to build a fresh surface.