Properties of thin a-Si:H and indium-tin oxide (ITO) layers as well as properties of interfaces of Si based heterojunction (HJ) ITO/(p)a-Si:H/n-Si structures were analyzed by means of atomic force microscopy (AFM) and scanning spreading resistance microscopy. It is shown that the morphology of thin ITO layers grown on n-type polished crystalline Si or on (p)a-Si:H/n-Si substrates depends on the deposition temperature and has peculiarities on nano-scale. Formation of highly conductive nano-dots on the surface and in the bulk of ITO layers is found. The observed nano-spots and nano-dots are attributed to the influence of hydrogen initiated reduction process, which occurs upon deposition of ITO films on an a-Si:H layer during the fabrication process of a HJ solar cell. This fact is confirmed by investigation of morphological properties of ITO surfaces after treatment by hydrogen plasma. It is shown that formation of conductive nano-particles on the ITO surface initiated by hydrogen does not change essentially transparency of an ITO layer. It is concluded that conductive nano-dots at the ITO/a-Si:H interface can be considered as local conductive channels, which provide a current flow through the ITO/(p)a-Si:H interface without essential shadowing of the solar cell structure. This finding opens an interesting way for the optimization of properties of the ITO/Si-based HJ solar cells.