A generic and universal layer engineering strategy for van der Waals (vW) materials, scalable and compatible with the current semiconductor technology, is of paramount importance in realizing all-two-dimensional logic circuits and to move beyond the silicon scaling limit. In this letter, we demonstrate a scalable and highly controllable microwave plasma based layer engineering strategy for MoS2 and other vW materials. Using this technique we etch MoS2 flakes layer-by-layer starting from an arbitrary thickness and area down to the mono- or the few-layer limit. From Raman spectroscopy, atomic force microscopy, photoluminescence spectroscopy, scanning electron microscopy and transmission electron microscopy, we confirm that the structural and morphological properties of the material have not been compromised. The process preserves the pre-etch layer topography and yields a smooth and pristine-like surface. We explore the electrical properties utilising a field effect transistor geometry and find that the mobility values of our samples are comparable to those of the pristine ones. The layer removal does not involve any reactive gasses or chemical reactions and relies on breaking the weak inter-layer vW interaction making it a generic technique for a wide spectrum of layered materials and heterostructures. We demonstrate the wide applicability of the technique by extending it to other systems such as graphene, h-BN and WSe2. In addition, using microwave plasma in combination with standard lithography, we illustrate a lateral patterning scheme making this process a potential candidate for large scale device fabrication in addition to layer engineering.