An improved substrate processing system. The system may be used for double sided scrubbing of a semiconductor substrate. The wet stations of the system has covers which prevent accumulated liquid from dripping outside of the station and which minimize dripping on the substrates. Transport tunnels are provided between modules to prevent leakage between the modules. A substrate transport mechanism which is moveable along a rail is provided with the stabilizer to provide for stable substrate transfer. The processing system has two brush stations which are placed within a single enclosure. The sensors located throughout the system, which sense the presence of a wafer, are fixedly mounted in a frame so that they are self-aligned to one another. In the sender station, two sensors are used, with the system requiring both sensors to sense the presence of a wafer to increase the reliability. In the dry station, the heating lamp is shielded from the substrate to reduce particulate contamination. Various flow meters are mounted on a transparent panel to provide easy and convenient hook-up. The system is provided with an airflow control bulkhead between the clean and dirty side of the system to prevent intermixing to thereby provide for lower contamination levels in the clean side of the system.