A confocal laser scanning microscope has been applied to the detailed study of non-invasive mapping on targeted systems. This paper aims to show, by particular reference to specific problems, the wide ranging potential of the technique for the analytical community. The specific problems successfully tackled by the technique include characterization of two types of inert support bodies and the precursor/enzyme distributions therein, the effect of processing on dye penetration in fibres, mapping the interdependence and growth patterns in bacterial colonies and non-invasive examination of epidermal tissue layers.