In the method of manufacturing a semiconductor device (1) with a semiconductor body (2), a doped zone (3) is formed in the semiconductor body (2). The semiconductor body (2) has a crystalline surface region (4), which crystalline surface region (4) is at least partly antorphized so as to form an amorphous surface layer (5). The amorphization is achieved by irradiating the surface (6) with a radiation pulse (7) which is absorbed by the crystalline surface region (4). The radiation pulse (7) has a wavelength which is chosen such that the radiation is absorbed by the crystalline surface region (4), and the energy flux of the radiation pulse (7) is chosen such that the crystal line surface layer (5) is melted. The method is useful for making ultra-shallow junctions.