An automatic material handling system comprising: (i) a storage stocker system having: - a stocker loading station (13, 103) for inputting or outputting substrate containers, operable alternatively manually or automatically, - a bare storage area (17, 102) for storing the substrates in bare form, - a robotic transfer (15, 201) for transferring substrates between the stocker loading station (13, 103) and the bare substrate area (17, 102), wherein the substrates within the containers are removed from the containers and stored bare in the bare substrate area (17, 102) and vice versa, (ii) an IO-buffer assembly, operable independently of the storage stocker system, having: - a buffer loading station (11, 104) adapted for holding a container, - one or more buffer stations (12, 101) for storing one or more containers containing substrates; - a buffer transfer mechanism to transfer containers between the buffer loading station (11, 104) and the buffer stations (12, 101); the automatic material handling system being characterized in that it further comprises (iii) an interface mechanism adapted for transferring directly a container between the one or more buffer stations and the stocker loading station (13, 103). (i) a storage stocker system having: - a stocker loading station (13, 103) for inputting or outputting substrate containers, operable alternatively manually or automatically, - a bare storage area (17, 102) for storing the substrates in bare form, - a robotic transfer (15, 201) for transferring substrates between the stocker loading station (13, 103) and the bare substrate area (17, 102), wherein the substrates within the containers are removed from the containers and stored bare in the bare substrate area (17, 102) and vice versa, - a stocker loading station (13, 103) for inputting or outputting substrate containers, operable alternatively manually or automatically, - a bare storage area (17, 102) for storing the substrates in bare form, - a robotic transfer (15, 201) for transferring substrates between the stocker loading station (13, 103) and the bare substrate area (17, 102), wherein the substrates within the containers are removed from the containers and stored bare in the bare substrate area (17, 102) and vice versa, (ii) an IO-buffer assembly, operable independently of the storage stocker system, having: - a buffer loading station (11, 104) adapted for holding a container, - one or more buffer stations (12, 101) for storing one or more containers containing substrates; - a buffer transfer mechanism to transfer containers between the buffer loading station (11, 104) and the buffer stations (12, 101); the automatic material handling system being characterized in that it further comprises - a buffer loading station (11, 104) adapted for holding a container, - one or more buffer stations (12, 101) for storing one or more containers containing substrates; - a buffer transfer mechanism to transfer containers between the buffer loading station (11, 104) and the buffer stations (12, 101); the automatic material handling system being characterized in that it further comprises (iii) an interface mechanism adapted for transferring directly a container between the one or more buffer stations and the stocker loading station (13, 103).