Bipolar transistors are the main element base in electronics. The development of this base was carried out mainly through experimentation. To justify the operation of the transistor, qualitative representations were used in the form of a double р–n junction of the р–n–p or n–p–n conductivity type. With this justification, many properties of a working semiconductor transistor remained beyond their clear understanding. Therefore, in this paper, the design of a bipolar transistor is considered, taking into account the structure of the solid body of the semiconductor base and the interaction of atoms in the form of negative ions with the surface of the solid body. Based on the analysis of data obtained by a tunneling microscope, the surface of the solid is covered with a monomolecular film, and the crystal of the semiconductor base itself is formed by positively charged atoms and is located under the monomolecular film. The molecular film is formed by surface clusters, and the crystal is formed by volume clusters. The interaction of surface clusters creates a porous structure of the molecular film. Through these pores the crystal of the solid body is visible. Impurities in the form of individual molecules penetrate the surface of the crystal through holes in the molecular film, formed in the form of columnar voids. On the surface of the crystal, impurity molecules, as a result of exchange interaction, dissociate into individual atoms, which in turn, also as a result of exchange interaction, are converted into negative ions. The doping of the surface of a semiconductor crystal of germanium or silicon with arsenic and indium molecules is specifically considered. After the molecules disintegrate into atoms in the columnar voids, they are converted into negative ions, which block the penetration of other molecules into these voids.