Science educators have generally agreed that understanding the atom concept is the basis of science education. However, the numerous research studies have shown that many students at all educational levels have difficulties understanding this concept. This study was developed under three headings. The first was to identify misconceptions that prospective teachers (PTs) had about atomic structure in the context of electrification by friction (ASCEF). The second was to study the effectiveness of the branch differences (basic sciences, social sciences, physics, chemistry, biology, mathematics) on the levels of their misconceptions. The third, based on students' misconceptions, was to examine the effectiveness of the activity "Modelling of the Atomic Structure" (MAS). The study was divided into two stages. First, in order to identify the PTs' misconceptions, an Understanding the Nature of Electrification by Friction Test (UNEFT) which could be summarised by the question "is electrification by friction due to the electron transfer?" was applied to the PTs who attended the Primary School Teacher Education Pedagogical Formation Certificate Program (PSTEPFCP) at a large public university for a five weeks science teaching course followed by an examination after the static electricity topic had been presented. It was found that the PTs from all branches of science held the misconception that electrification by friction was due to the transfer of protons. At the same time the effects of the branch differences on the levels of the PTs' misconceptions was studied and was not significant in groups other than the basic scientists-social scientists pairing. In the second stage, using the students' misconceptions, the effectiveness of the MAS activity was examined in the experimental and control groups and was found to be significant at all levels. From this result, it was found that the models were quite useful in teaching science and that the construction of knowledge would be possible if students played an active role in the learning environment. (Contains 13 tables and 7 figures.)