The present invention provides an electrochemical deposition system that is designed with a flexible architecture that is expandable to accommodate future designs and gap fill requirements and provides satisfactory throughput to meet the demands of other processing systems. The electrochemical deposition system generally comprises a mainframe having a mainframe wafer transfer robot, a loading station disposed in connection with the mainframe, one or more processing cells disposed in connection with the mainframe, and an electrolyte supply fluidly connected to the one or more electrical processing cells. Preferably, the electrochemical deposition system includes a spin-rinse-dry (SRD) station disposed between the loading station and the mainframe, a rapid thermal anneal chamber attached to the loading station, and a system controller for controlling the electrochemical deposition process and the components of the electrochemical deposition system.