This work describes the application of laser ion source (LIS) for fabrication of semiconductor nanostructures, as well as relevant equipment completed and tested in the IPPLM for the EU STREP “SEMINANO” project and the obtained experimental results. A repetitive pulse laser system of parameters: energy of ∼0.8 J in a 3.5 ns-pulse, wavelength of 1.06 μm, repetition rate of up to 10 Hz and intensity on the target of up to 1011 W/cm2, has been employed to produce Ge ions intended for ion implantation into SiO2 substrate. Simultaneously, laser-ablated material (atoms clusters debris) was deposited on the substrate surface. The parameters of the Ge ion streams (energy and angular distributions, charge states, and ion current densities) were measured with the use of several ion collectors and an electrostatic ion energy analyzer. The SiO2 films of thickness from 20–400 nm prepared on substrates of a single Si crystal were deposited and implanted with the use of laser-produced germanium of different properties. The modified SiO2 layers and sample surface properties were characterized with the use of different methods: X-ray photoelectron and Auger electron spectroscopy (XPS+AES), Raman scattering spectroscopy (RSS) and scanning electron microscopy (SEM). The production of the Ge nano-crystallites has been demonstrated for annealed samples prepared in different experimental conditions.