A system for processing substrates in plasma chambers, such that all substrates transport and loading/unloading operations are performed in atmospheric environment, but processing is performed in vacuum environment. The substrates are transported throughout the system on carriers. The system's chambers are arranged linearly, such that carriers move from one chamber directly to the next. A conveyor, placed above or below the system's chambers, returns the carriers to the system's entry area after processing is completed. Loading and unloading of substrates may be performed at one side of the system, or loading can be done at the entry side and unloading at the exit side.