Precise microstructuring of silicon with short laser pulses is a promising technique for fabrication of kinoform diffractive optical elements (DOEs) for high-power THz radiation. Micrometer-scale surface roughness being a typical result of the silicon microstructuring with laser is an important factor reducing optical performance of the fabricated DOEs. We demonstrate here that proper optimization of the processing conditions under profiling of high-resistance silicon surface by 1 ps laser pulses at λ = 1.03 μm allows formation of cylindrical Fresnel lens with the surface roughness of 0.5–1.2 µm being one order of magnitude smaller than reported earlier. Testing of the fabricated lens with a free electron laser at the wavelength of 141 μm has shown that the laser-machined silicon retains its original transmittance. Diffraction efficiency (0.93 ± 0.06) and deviation of the laser intensity profile in the lens focus from the theoretical expectations have been evaluated. Additionally, influence of the surface roughness on transmittance of the laser-machined silicon in the wavelength range of 95–400 μm was studied by means of time domain spectroscopy.