From clay model to 3d printed model

I created a 3d model of a protoype object using clay.
Then I scanned it, both by Autocad 123d Catch and SCANN3d for Android.
In both cases I get coarse results.
Now I need to:
- smooth surfaces
- close holes
- refine some parts

I'm quite skilled with Sketchup... but it requires segment-by-segment and dot-by-dot editing, as I can't find suitable/powerful plugins to perfomr these task.
My object is all but geometric; it has lot of irregular surfaces.

What's the best free program to edit/sculpt it?

Consider it's kind of a handle which must "suite" to the shape of the interior of my hand palm, but not with millimeter precision, it just has to have an "ergonomic surface".

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