For formation of micro-cones on a surface of a semiconductor very often are used femtosecond laser induced plasma [1] or chemical vapor depositions with catalytic metal on Si [2]. We propose another method for formation of micro-cones by basic frequency of microsecond Nd:YAG on Ni/Si structure. It was observed self-organization of cone-like microstructures on a surface of Si with Ni covered layer with thickness 30 nm by Nd:YAG laser beam at threshold intensity 3.15 MW/cm2. The structural and optical characteristics of micro-cones where studied by optical microscope, scanning electron microscope (SEM) and Raman back scattering spectroscopy. Optical microscopy study of the irradiated sample surface by Nd:YAG laser beam has shown formation of islands with diameter less than 1 m. The micro-chemical analysis by means of SEM has shown that the islands consist of NiSi2 or Ni. It means the new phase of NiSi2 is formed. An evidence of our suggestion is appearance of phonon line at 225 cm-1 attributed to Ni-Si vibration in Raman back scattering spectrum. The further increase of the laser intensity and number of laser pulse leads to formation of cone-like microstructures with Ni on the top of cone and maximal height up to 100 m. The control of micro-cone shape and height was achieved by changing laser radiation intensity and number of pulses. Irradiated region of the structure with maximal intensity 4.5 MW/cm2 and 22 numbers of pulses, becomes black. Experimentally we have found a possibility to form “black” silicon for solar cells and silicide - NiSi2 for microelectronics by laser radiation.