Direct Laser Writing (DLW) and X-ray computed tomography (XCT) both offer unique possibilities in their respective fields. DLW produces full three-dimensional (3D) polymer structures on the microscale with resolutions below 100 nm. The fabricated structures can be analysed by XCT or X-ray microscopy (XRM), which incorporates additional X-ray lenses, in three dimensions down to a minimal basic spatial resolution of about 500 nm or 50 nm, respectively. In this work, two different DLW structures are analysed via XCT. Internal defects are detected and analysed for the purpose of quality control. Defects and structures with sizes down to 1.5 µm are successfully analysed. A 3D reconstruction and internal, hidden features of the fabricated structures are shown and discussed. In a first-of-its-kind study, we demonstrate the detectability of a single-voxel line inside a fabricated structure that would not be detectable with SEM or light microscopy. Furthermore, the direct fabrication on a PET substrate is shown to overcome the high X-ray absorbance of commonly used glass substrates. Attenuation spectra of SZ2080 and glass substrates are compared to a fabrication route direct on a 170 µm PET foil. The practical aspects of XCT measurements for DLW structures on different substrates will be discussed.