How to filter or eliminate earths magnetic field readings around 3D Magnetic sensor?
Earth magnetic field is pretty constant. In your measurements it will show up as an offset that you could subtract, but of course it will change if the sensor rotates.

Whatever measurement noise you see certainly doesnt' come from Earth. Either your setup is close to a local source of magnetic radiation (inductors, wires with high alternating current), or your sensor picks up noise from its power supply. Put your sensor away from high currents, power it with batteries and see how much noise you'll get in that case.