The method comprises blanket depositing a layer of a first material on a semiconductor structure, on the surface of which protruding regions (34A) have been formed bordering with a vertical wall (40) on adjacent areas, and subsequently removing completely or selectively that layer by reactive ion etching where prior to the deposition of said layer the vertical wall (40) is reshaped either by removing material from that wall (40) or by accumulating a second material on said wall (40). The method prevents that uncontrolled residues of materials like a doped polysilicon after reactive ion etching steps. These residues might be detrimental to devices and elements, like transistors and resistors formed in the semiconductor substrate.