We report the experimental results of X-ray computed tomography (X-CT) of directed self-assembly (DSA) formed metal-containing nanocylinders with a width in the range of 25–30 nm. We compare the X-CT results for DSA formed metal nanowires inside deep Si trenches with those of conventional morphological characterization techniques such as scanning electron microscopy (SEM) and transmission electron microscopy (TEM). It is found that X-CT is more reliable than SEM and TEM, especially when analyzing the 3D nanometer-sized structures embedded in the organic matrix.