The micro-profile, elemental composition, and positive etching wedge formed during the Bosch process of through micro-holes in silicon wafers are investigated by methods of optical and scanning electron microscopy, energy dispersive spectroscopy and optical profilometry. The maximum height of the wall profiles is shown to be 3.1 μm at a base length of 100 μm. The dynamics of the positive etching wedge forming on the boundary silicon–polyimide is studied. The most intense etching occurs at the micro-hole center; the wedge’s geometric dimensions (the depth, external diameter and tilt angle) linearly increase in proportion to the number of etching cycles. The elemental composition of the micro-hole surfaces after their formation and also after additional processing is experimentally investigated. It is shown that the sequential removal of polyimide from oxygen plasma and aluminum in liquid etchant does not lead to micro-hole surface contamination. © 2017, Pleiades Publishing, Ltd.