manged to produce workable solid from scanned 3D object, now what?

This seems like a frequently asked question.
After following some advice from here:
I produced a simplified mesh, from which i created a solid in FreeCAD, but still- how can I manipulated further- ie: there are holes in the surface, where the stickers used for orienting the scanner were, and using different functions I was unable to fill them easily.
Any advice?

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