In the paper a possibility of using a metrology micro computed tomography (CT) to assess quality of parts made by rapid prototyping technique was presented. Additive manufacturing techniques dramatically change the approach to manufacturing process. Not long ago they allowed solely for obtaining a spatial model of a part in order to visualize its features. Nowadays, it is possible to produce elements and assembly groups with properties that make it possible to replace many parts manufactured using traditional casting or injection techniques. Polymer components created by means of 3D printing can be generated one layer of material after another. In many cases inner spaces (sections) are not fully filled in (solid), they are rather replaced by a specially selected structure. Thanks to this it is possible to save material and reduce weight. To control these structures and to inspect joints between particular layers using a non-destructive method it is necessary to use a metrology micro CT. In the paper an application of X-ray computed tomography and assessment of measurement uncertainty regarding elements manufactured with fused deposition modeling (FDM) method using ABS 3D printing on UP! printer was presented. Inspection of both: inner structure and outer shapes as well as joints between them was performed basing on computer aided design (CAD) model.