The invention provides a method of processing a wafer using multilayer processing sequences and Multi-Layer/Multi-Input/Multi-Output (MLMIMO) models and libraries that can include one or more measurement procedures, one or more Poly-Etch (P-E) sequences, and one or more metal-gate etch sequences. The MLMIMO process control uses dynamically interacting behavioral modeling between multiple layers and/or multiple process steps. The multiple layers and/or the multiple process steps can be associated with the creation of lines, trenches, vias, spacers, contacts, and gate structures that can be created using isotropic and/or anisotropic etch processes.