Matrix-assisted pulsed laser evaporation (MAPLE) has been recently developed to deposit high-quality thin films for a wide range of polymeric materials. To analyze the evaporation of polymer molecules in MAPLE, we present a molecular dynamics (MD) simulation of laser ablation where the target material is modeled as a solution of polymer molecules in a molecular matrix. The breathing sphere model is used for MD simulations of laser ablation of the molecular matrix. Polymer molecules are described using a bead-spring model, where each bead represents one or several polymer groups. The initial stage of polymer ejection is investigated at different laser fluences and pulse durations. The influence of polymer molecules on the stability of clusters formed in the plume and the processes that can lead to polymer decomposition are discussed.