Embodiments of the invention generally relate to systems and methods to CMP substrates. The systems generally include a polishing system that has a polishing module and cleaning module. Each of the polishing module and the cleaning module can be partitioned into independently operable sections. Each section of the polishing module includes a platen, at least one load cup, and at least one polishing head. Each section of the cleaning module includes a cleaning station and one or more robots adapted to advance substrates through the cleaning station. The methods generally include polishing a plurality of substrates in a polishing system having independently operable sections. During the polishing of the substrates in one section, a second of the independently operable stations may be maintained or cleaned.