Ultrathin films (6–10 nm) of silver and nickel were deposited by pulsed laser deposition (PLD) in high vacuum (1 × 10−6 mbar). Microstructural evolution of these films as function of incident laser energy, substrate temperature, substrate material [borosilicate glass, fused silica, MgO(100) and Si (311)] and target–substrate distance was studied in detail using dynamic force microscopy. It is shown that with increase in laser energy incident on the target, there is a substantial increase in particle size in the film. The effect of increased laser energy on microstructure is much more drastic than that for the increase of substrate temperature. In general, denser packing of nanoparticles and increased clustering have been observed at elevated substrate temperature. Increase in laser energy gives rise to higher average grain size, packing density, and clustering in comparison to substrate temperature. It is observed that the aspect ratio of grains is dependent on incident laser fluence and substrate temperature, but more drastically on the substrate material. Substrate coverage and aspect ratio of the grains are particularly dependent on the nature of crystallinity of the substrates. It is demonstrated that PLD provides a greater degree of microstructural manipulation than other physical vapor deposition techniques.