Method and system for isolated and discretized process sequence integration

A method for combinatorially processing a substrate in a cluster tool, comprising method operations of:

• receiving the substrate;
• successively processing multiple layers within site-isolated regions of the substrate while spatially varying a mask between the successive processing of the multiple layers to vary a size relationship between the multiple layers, wherein spatially varying the mask between the successive processing comprises:
• processing the substrate in a chamber of the cluster tool with a first mask having a first feature set;
• removing the first mask having the first feature set from the chamber into a module of the duster tool;
• removing a second mask from the module into the chamber, wherein the removing the first mask and removing the second mask occurs without breaking vacuum within the chamber or the module;
• transitioning a shutter to extend into the chamber from a shutter garage coupled to the chamber, the shutter blocking a portion of the second mask;
• and
• processing the substrate in the chamber with the second mask having the second feature set.