Thin films synthesized by assembling clusters present interesting chemical and physical properties and a large specific surface, and are appealing for functional applications (e.g. sensing and catalysis). Also, clusters supported on surfaces are interesting both for nanocatalysis applications and for fundamental research. By means of pulsed laser deposition (PLD) in a background atmosphere we can induce cluster aggregation in the ablation plume and control the deposition kinetic energy of the clusters. These phenomena depend on the plume expansion dynamics and their influence on the properties of the deposited films has been investigated as a function of the background gas mass and pressure. The control of these parameters permits variation of the film surface morphology, from a compact structure with a very smooth surface, to a film with a controlled roughness at the nanoscale, to an open, low density meso- and nanostructure characterized by a high fraction of voids and by a large specific area. Thin films of WOx, TiOx, Pd/PdO, and Ag were deposited and characterized by atomic force microscopy (AFM), scanning electron microscopy (SEM) and Raman spectroscopy. Post-deposition annealing permits control of the crystalline degree of the films, which in the case of tungsten and titanium oxide is found to depend on the original nanostructure, while a different degree of oxidation can be induced by controlling the amount of oxygen in the deposition chamber. In-situ scanning tunneling microscopy (STM) was employed to study the first stages of growth of W films on different substrates. This opens the possibility to tailor the material properties through the control of the building nano-units.