Thin polymer films are deposited using matrix-assisted pulsed-laser evaporation and subsequently are characterized by scanning electron and atomic force microscopies. An Er : YAG laser (2937 nm, 350 μs) is used as a light source and the effect of the energy density supplied by the laser on the morphology of the deposited films is investigated. It is found that the appearance of undesirable non-uniform morphological features arises from either poor solubility of the guest molecules or insufficient energy density provided by the laser to vaporize the entire ejected volume. In addition, the surface roughness of two guest–host systems is found to depend linearly on the polymer concentration. These results allow us to better understand earlier work in the field and to establish a framework by which MAPLE films may be improved.