Self-assembled indium deposition-induced nanostructures are obtained on the UHV cleaved (100) surface of In$_4$Se$_3$ layered semiconductor crystals. The small indium-deposition rates and short deposition times are chosen to study growth orientation and origin of nanostructures observed by scanning tunnelling microscopy (STM) on the (100) surface of In$_4$Se$_3$ after indium deposition. The shape of these nanostructures strictly depends on the overstoichiometric indium concentration level in the melt during the crystal growth varying from 3$D$ islands for low concentration to elongated shapes, i.e., nanowires, in the case of highly-indium-doped crystals. High-resolution STM study determines the self-assembled quasi-periodical nanowires’ growth along $c$-axis of (100)In$_4$Se$_3$ substrate. The spatially resolved scanning tunnelling spectroscopy (STS) study revealed metallic nature of the surface of nanostructures grown on the semiconductor substrate. The growth mechanism of indium-deposited nanostructures is considered to be powered by anisotropic striated lattice structure of In$_4$Se$_3$ (100) surface with indium nucleiin concentration depending on the degree of overstoichiometric crystal-growth indium subsequently intercalated into the interlayer gap.