Substrate processing systems and methods are described for site-isolated processing of substrates. The processing systems include numerous site-isolated reactors (SIRs). The processing systems include a reactor block having a cell array that includes numerous SIRs. A sleeve is coupled to an interior of each of the SIRs. The sleeve includes a compliance device configured to dynamically control a vertical position of the sleeve in the SIR. A sealing system is configured to provide a seal between a region of a substrate and the interior of each of the SIRs. The processing system can include numerous modules that comprise one or more site-isolated reactors (SIRs) configured for one or more of molecular self-assembly and combinatorial processing of substrates.