Laser irradiation of Ge quantum dots (QDs) grown on Si(100) substrates by solid-source molecular beam epitaxy has been performed using a Nd:YAG laser (532 nm wavelength, 5 ns pulse duration) in a vacuum. The evolution of the Ge QD morphology, strain and composition with the number of laser pulses incident on the same part of the surface, have been studied using atomic force microscopy, scanning electron microscopy and Raman spectroscopy. The observed changes in the topographical and structural properties of the QDs are discussed in terms of Ge-Si diffusion processes. Numerical simulations have been developed for the investigation of the temperature evolution of the QDs during laser irradiation. The obtained results indicate that the thermal behaviour and structural variation of the nanostructures differ from conventional thermal annealing treatments and can be controlled by the laser parameters. Moreover, an unusual island motion has been observed under the action of subsequent laser pulses.