Scanning tunneling microscopy (STM) imaging has been performed on the HPI layer (hexagonally packed intermediate layer), freeze‐dried and coated with Pt–Ir–C. The HPI layer is a highly corrugated regular protein monolayer, found outermost in the cell wall of the bacterium Deinococcus radiodurans. The average structure of each of the two surface aspects of HPI layer has been determined from STM data using correlation averaging. The signal‐to‐noise ratio of the raw data obtained from STM of the HPI layer is in the range of 1.5 to 2, values much higher than those usually encountered in data obtained by transmission electron microscopy (TEM). In order to discuss reliability and accuracy of STM imaging, the reliefs obtained by STM are compared to reconstructed reliefs derived from TEM micrographs of freeze‐dried and metal‐coated specimens.