Abstract: We present the state-of-art detection method of three-dimensional vortices and apply it to realistic magneto-convections simulations performed by the MURaM code. The detected vortices extend from the photosphere to the low chromosphere, presenting similar behaviour at all height levels. The vortices concentrate the magnetic field, and thereby the plasma dynamics inside the vortex is considerably influenced by the Lorentz force. Rotational motions also perturb the magnetic field lines, but they lead to only slightly bent flux tubes as the magnetic field tension is too high for the vortex flow to significantly twist the magnetic lines. We find that twisted magnetic flux tubes are created by shear motions in regions where plasma-beta>1, regardless of the existence of flow vortices.