Micro-CT and especially nano-CT scanning requires very high mechanical precision and stability of object manipulator, which is difficult to reach. Several other problems, such as drift of emission point inside an X-ray source, thermal expansion in different parts of the scanner, mechanical vibrations, and object movement or shrinkage during long scans, can also contribute to geometrical inaccuracies. All these inaccuracies result in artifacts which reduce achievable spatial resolution. Linear distortions can be partially compensated by rigid X/Y shifts in projection images. More complicated object movement and shrinkage will require non-linear transforms. This paper investigates techniques to compensate geometrical inaccuracies by linear transformation only. We have developed two methods to estimate individual X/Y shifts in each measured projection. The first method aligns measured projections with forward-projected projections iteratively to reach an optimal X/Y shift estimation. It is more suitable for mechanical inaccuracies caused by random and jittery movement. The second method uses a very short reference scan acquired immediately after a main scan to obtain estimates of X/Y shifts. This method is rather effective for mechanical inaccuracies caused by slow and coherent mechanical drifts. Both methods have been implemented and evaluated on multiple scanners. Significant improvements in image quality have been observed.© (2008) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.