A modular gas box system comprises a series of modules that each connect into upper and lower manifolds that distribute reactive and purge gases through weldments and monoblock valves. A motherboard distributes power, control signals, and pneumatics air to all the plug-in modules. Environmental modules provide vent and purge lines to the process' reaction chambers. An embedded microcomputer manages in situ system and safety diagnostics for each and every module that has been assigned a motherboard address. Each gas module 24 is easy to remove and replace and the pneumatics control motherboard integrates pneumatics distribution, analog-to-digital converters, device controllers and support electronics. Gas module 24s include digital mass flow controllers, analog and digital pressure switches and transducers, gas filters and pneumatic valves.