Low frequency and low intensities magnetic and electric fields are used in physiotherapy for a long time. But due to the fact that the action of these fields on living tissues is very complicated and at the moment insufficiently studied, nowadays there is no simple method to measure their curative effect. In practrice the natural way of investigations is the experimental one: to observe the state of a patient during curative sessions and collect statistical data. We propose to combine practical approach with the study of processes in external environment when low intensity magnetic fields act. With this purpose we calculate and visualize the trajectories of ions in electromagnetic field generated by a magnetotherapy device. Such an approach leads to obtaining a series of images that show trajectories depending of the choice of the parameters of the device. That results in visual representation of typical phase portraits generated by the applied mathematical model. Visual perception helps to compare the number of procedures, parameters of the used device and the changing of patient state, and thus to form an expert knowledge in this area.