The disclosure is directed to techniques in preparing an atom probe tomography (“APT”) specimen. A structure in a semiconductor device is identified as including a test object for an APT procedure. A target region is identified in the structure where an APT specimen will be obtained. The target region is analyzed to determine whether a challenging component feature exists therein. A challenging component may include a hard-to-evaporate material, a hollow region, or a material unidentifiable with respect to the test object, or other structural features that pose a challenge to a successful APT analysis. If it is determined that a challenging component exists in the target region, the challenging component is replaced with a more suitable material before the APT specimen is prepared.