In the present work, the influence of the secondary fluorescence enhancement in confocal X-ray microscopy analysis is studied when stratified type of materials are examined. Through a proper mathematical formalism, an exact global theoretical model is presented which accounts for the secondary fluorescence enhancement when either particle (3D-Micro particle induced X-ray emission) or photon (3D-Micro X-ray fluorescence) microbeams are used in the excitation channel. The contribution of the secondary fluorescence effect to the confocal X-ray intensity profiles was calculated for some typical representative cases. In addition, the influence of several experimental parameters was examined in terms of their influence in the absolute intensity and shape of the secondary fluorescence intensity profile.