In this work is presented a part of bigger research that is dealt with the instructive treatment of conceptual obstacles of students of Pedagogic Department that is connected with the Quantum Atomic Model (QAM), as they are revealed by the bibliographic research and the pilot empirical study. It is also described the development of an educational software `The Quantum Atom' as Educational Virtual Environment (EVE), which was used for the instructive treatment of one of the five "obstacles - targets". This conceptual obstacle is connected with the visualization of isosurface density plots and electron density plots for different energy situations of the atom. During their interaction with the EVE the students are conducted to an intellectual conflict for the destabilization of the obstacle and the construction of a conceptual representation of the atom according to Quantum Mechanics. The qualitative analysis of our results shows that EVEs characteristics, as the three-dimensional dynamic visualizations and user's interaction, seem to play an important role in learning outcomes.