The invention provides a method of processing a wafer, which uses ion energy (IE)-related multilayer process sequences and ion energy controlled multi-input/multi-output (IEC-MIMO) models and libraries that can include one or more measurement procedures, one or more IEC-etch sequences, and one or more Ion Energy Optimized (IEO) etch procedures. The IEC-MIMO process control uses dynamically interacting behavioral modeling between multiple layers and/or multiple IEC etch sequences. The multiple layers and/or the multiple IEC etch sequence can be associated with the creation of lines, trenches, vias, spacers, contacts, and gate structures that can be created by using IEO etch procedures.