Three-dimensional (3D) reconstruction methods generate a 3D textured model from the combination of data from several captures. As such, the geometrical transformations between these captures are required. The process of computing or refining these transformations is referred to as alignment. It is often a difficult problem to handle, in particular due to a lack of accuracy in the matching of features. We propose an optimization framework that takes advantage of fiducial markers placed in the scene. Since these markers are robustly detected, the problem of incorrect matching of features is overcome. The proposed procedure is capable of enhancing the 3D models created using consumer level RGB-D hand-held cameras, reducing visual artefacts caused by misalignments. One problem inherent to this solution is that the scene is polluted by the markers. Therefore, a tool was developed to allow their removal from the texture of the scene. Results show that our optimization framework is able to significantly reduce alignment errors between captures, which results in visually appealing reconstructions. Furthermore, the markers used to enhance the alignment are seamlessly removed from the final model texture.