The study was conducted in a production company operating in the wood processing industry. Geometric characteristics of input material were captured and used to derive statistical distributions, which were then included in the simulation model. The conducted experiments indicated that the quality of the simulation model was significantly affected by the quality and quantity of the sample, on the basis of which the stochastic model is estimated. It was shown that small sample for wood processing data was insufficient to capture process variability. On the other hand, excessive sample size (80 or more observations) for the material with high natural geometric variability, involves taking into account outliers, which may lower the overall prognostic quality of the simulation model. Based on the conducted simulation experiments, the recommended sample size which allows development of a reliable model for estimation of material loss in the analyzed manufacturing process, ranges from 40 to 60 measurements.