We developed a control system for an electron cyclotron resonance plasma enhanced chemical vapor deposition (ECR-PECVD) reactor for the growth of inhomogeneous dielectric thin films for optical applications. The system supervises the growth of Alms of a required refractive index profile on different substrates including optical fiber ends. It controls the gas flow rates, microwave power, radio frequency substrate bias, and the ECR and extraction magnet power supplies. The system also adjusts the microwave generator to minimize reflected power during deposition. The characteristics of the ECR-PECVD system and the automation of the deposition process are discussed using the growth of a complex rugate optical filter as an example.