In a grazing incidence X-ray diffuse scattering investigation of boron implanted silicon we have discovered narrow intensity streaks along directions. From a detailed analysis of three dimensional reciprocal space maps clear evidence is found that the rod-like scattering is due to extrinsic stacking faults with an average diameter of 71nm, formed in the implanted layer after rapid thermal annealing. At the same time nanometer sized features appear at the Si surface which are characterized by atomic force microscopy and specular reflectivity measurements.