As both opencv and pcl libraries will be included in a larger code in the future, the conflict has been avoided using the following trick: create a file cv_compatible.h in the same directory as cv.h (typcally /usr/include/opencv/) containing the same code as in cv.h, but comment the line #include opencv2/flann/flann.hpp (with quotes). The file cv_compatible.h is in the docs/ foler of the project. As a consequence, added smoothing functions using MLS in PostProcessor class.