All these tips are super useful, thank you all very much for the contribution to this discussion!
I already used some of them, however none of them can fix the bumpiness of the surface all the time, it depends on how the control points are at the initial configuration, and how is the conformation of the surface that you want to preserve. The main problem is that any type of smooth does not consider the curvature of the surface around the smothened area, but only the coordinates of adjacent vertices.
From a mesh editing point of view in some software there is a command called Edge flow which might be what I actually need most of the times.
you can download the free plugin for Blender here, if you are interested.
Having something like this into rhino to control CPs would be gamechanging.