We investigated the non-periodic nano-structural modulation of crystalline silicon surface enabled by a tightly focused ultrashort pulse laser. The focused annular beam reduces the cross-sectional area of electron multiplication to be smaller than the wavelength of the surface electromagnetic wave which is represented by the surface plasmon polaritons. The silicon wafer surface was amorphized with a consistent narrow line profile beyond the diffraction limit by suppressing the formation of the LIPSS-induced side ripples. We also revealed that the important excitation of free carriers by an ultrashort pulse shorter than 1.7 ps leads to the amorphization below the ablation threshold, thereby bulged uniformly in the range of 6-28 nm with a sub-micron linewidth. This structural change shows its potential applications in nanoscale surface structuring with advanced heightcontrollability in the nanometer-scale.