mat = Orthogonalize[RandomReal[{0, 1}, {3, 3}]]; Graphics3D[GeometricTransformation[Cuboid[], mat]]
I wish to get this transformation:
I'd rather not make assumptions about what you mean by "change the reference system". Maybe you can provide a before and after comparison so I know what you're trying to change.
I am not sure what you mean. I would consider GeometricTransformation for a general linear change, Translate or Rotate for more specific changes.