A low profile, compact atomic layer deposition reactor (LP-CAR) has a low-profile body with a substrate processing region adapted to serve a single substrate or a planar array of substrates, and a valved load and unload port for substrate loading and unloading to and from the LP-CAR. The body has an inlet adapted for injecting a gas or vapor at the first end, and an exhaust exit adapted for evacuating gas and vapor at the second end. The LP-CAR has an external height no greater than any horizontal dimension, and more preferably no more than two-thirds any horizontal dimension, facilitating a unique system architecture. An internal processing region is distinguished by having a vertical extent no greater than one fourth the horizontal extent, facilitating fast gas switching. In some embodiments one substrate at a time is processed, and in other embodiments there may be multiple substrates arranged in the processing region in a planar array. The compact reactor is distinguished by individual injectors, each of which comprise a charge tube formed between a charge valve and an injection valve. The charge valve connects the charge tube to a pressure regulated supply, and the injection valve opens the charge tube into the compact reactor. Rapidly cycling the valves injects fixed mass-charges of gas or vapor into the compact reactor. Multiple such compact reactors are stacked vertically, interfaced into a vacuum handling region having a Z-axis robot and a load/unload opening.