We have constructed a compact prototype apparatus for active correction of circle of confusion during rotational motion. Our system combines fiber optic interferometry as a sensing element, the reference cylinder along with the nanopositioning system, and a robust correction algorithm. We demonstrate dynamic correction of run-out errors down to 40 nm; the resolution is limited by ambient environment and accuracy of correcting nanopositioners. Our approach provides a compact solution for in-vacuum scanning nanotomography x-ray experiments with a potential to reach sub-nm level of correction.