Abstract This paper discusses the implementation of GHz-Scanning Acoustic Microscopy (GHz-SAM) into a wafer level scanning tool and its application for the detection of delamination at the interface of hybrid bonded wafers. It is demonstrated that the in-plane resolution of the GHz-SAM technique can be enhanced by thinning the sample. In the current study this thinning step has been performed by the ion beam of a ToF-SIMS tool containing an in-situ AFM, which allows not only chemical analysis of the interface but also a well-controlled local thinning (size, depth and roughness).