Derivative technology like embedded Non-Volatile Memories (eNVM) is raising new types of challenges on the “more than Moore” path. By its construction: overlay is critical across multiple layers, by its running mode: usage of high voltage are stressing leakages and breakdown, and finally with its targeted market: Automotive, Industry automation, secure transactions… which are all requesting high device reliability (typically below 1ppm level). As a consequence, overlay specifications are tights, not only between one layer and its reference, but also among the critical layers sharing the same reference. This work describes a broad picture of the key points for multilayer overlay process control in the case of a 28nm FD-SOI technology and its derivative flows. First, the alignment trees of the different flow options have been optimized using a realistic process assumptions calculation for indirect overlay. Then, in the case of a complex alignment tree involving heterogeneous scanner toolset, criticality of tool matching between reference layer and critical layers of the flow has been highlighted. Improving the APC control loops of these multilayer dependencies has been studied with simulations of feed-forward as well as implementing new rework algorithm based on multi-measures. Finally, the management of these measurement steps raises some issues for inline support and using calculations or “virtual overlay” could help to gain some tool capability. A first step towards multilayer overlay process control has been taken.