We developed an autonomous modeling system for the calculation processes of the simulator for film deposition processes in order to decrease the calculation cost for reproducing experimental results. Replacing the simulator with the mathematical models proposed by the modeling system decreased huge calculation cost of the simulator. The system consists of one mobile agent and three platforms for the agent. The agent autonomously moved in the computer-networks and operated the process simulator in the platform in order to make training data needed for modeling and then operated the generalized modeling software in the platform using the training data and finally the agent created the models. The models showed both good reproducibility and predictability with the calculated results of the simulator.