This study is a part of a Swarm CubeSat mission presently designed in Skoltech. We present a low-cost magnetic cleanliness routine for CubeSats to minimize the produced disturbances during the steps of design and assembly along with constructing the spacecraft-specific disturbance model which is subsequently used in the attitude determination and control loop of the CubeSat. We are using in-house software to calculate the magnetic disturbances due to currents flowing through electric components. The procedure imports the designed components of the CubeSat and then calculates the electrical participation into both disturbances mentioned before. As a modeling advantage, it can be used for each operation regime of the CubeSat to make sure that the overall varying disturbances are continuously known. With the knowledge of magnetic disturbance quantities for different regimes, it is possible to construct a representative magnetic dipole moment which is to be utilized in the design process along with in orbit simulation to represent the results in the case of full CubeSat operation. A simulation of the CubeSat in orbit is conducted to investigate the pointing accuracy using the calculated torque and magnetic field as disturbance parameters. The simulation uses an Extended Kalman Filter to estimate the varying magnetic disturbance along with the standard set of rotational dynamics state variables. The same estimation algorithm is to be implemented in the CubeSat's flight software.