Abstract The Mn and Fe deposited clean Si(1 1 1) substrates were examined with UHV-TEM and STM that are part of an UHV-TEM/STM integrated characterization system. The Mn deposition with coverages of 5–20 ML followed by annealing at 673 K for 5 min formed MnSi islands. STM image revealed their surface √3×√3 structure. The re-deposition of 10–20 ML Mn and re-annealing at 573 K for 5 min succeeded to transform the MnSi islands into MnSi 1.7. The Fe deposition with coverages of 5–20 ML followed by annealing at 873 K for 5 min formed β-FeSi 2 islands. TEM image of these islands showed Moire fringes in different directions.