When applied to 3D image reconstruction, conventional landmark-based registration methods tend to generate unnatural vertical structures due to inconsistencies between the employed model and the real tissue. This paper demonstrates a fully non-rigid image registration method for 3D image reconstruction which considers the spatial continuity and smoothness of each constituent part of the microstructures in the tissue. Corresponding landmarks are detected along the images, defining a set of trajectories, which are smoothed out in order to define a diffeomorphic mapping. The resulting reconstructed 3D image preserves the original tissue architecture, allowing the observation of fine details and structures.