Atom probe tomography (APT) is a very suitable technique for chemical analysis on the atomic level. However, the time-consuming site-specific preparation of special regions of interest (ROI), such as grain boundaries can be improved. Recently, transmission Kikuchi diffraction (TKD) has been applied successfully for high resolution crystallographic analyses of thin foils by using a standard electron backscatter diffraction detector and a commercial software. We present the successful application of the combined focused ion beam (FIB)/TKD preparation of site-specific APT specimens by several examples in the research topic of high performance metal based materials. It will be shown that the APT tip preparation process in special regions of interest can be substantially accelerated by TKD analyses in-between the annular milling FIB procedure in the same microscope. With this combined method, a ROI can easily be recognized and positioned in the first 200 nm of an APT sample much faster than e.g. with correlative transmission electron microscope investigations. Even more, the high resolution technique of TKD gives the opportunity to get crystallographic information of the mapped area. Moreover, the crystallographic information can be used to optimize the reconstruction of the APT data.