This feature is called optical sectioning. True, three-dimensional data sets can be recorded. Due to the small dimension of the illuminating light spot in the focal plane, stray light is minimized. By image processing, many slices can be superimposed, giving an extended focus image which can only be achieved in conventional microscopy by reduction of the aperture and thus sacrificing resolution. Confocal Microscopy is not without its problems Excitation of the entire sample for each scan can cause photo-bleaching or quenching of the fluorescent signal.
Thick specimens lose details in the Z-plane.
Just like conventional fluorescent microscopy bleed through of one channel to another in multi-labeled samples can be a problem. Natural auto fluorescence can interfere with a labeled signal. To avoid photobleaching from single photon systems, a new generation of microscopes have been developed. Together their energy excites the fluorochrome molecule. In addition, the optical path of the two photon system reduces light scatter which allows deeper scans of samples with less loss of detail.