If you have rough edges on the dies you can easily sand them without any damage to the die as long as it is not the cutting edge of the die. That would distort the edge and you may not get good cuts any longer.
The original Nestabilities, once called Geometrics, that Spellbinders has had since the beginning of the company, were nested but during the manufacturing process all the shapes in each set were held together at the bottom and top by a small tang of metal. You would twist them apart. This left the little bits of metal from the tangs. I would either sand them or use a wire cutter to get them off if they bothered me. It's great that they are now doing them without the tangs. Just saves a step.