The Confocal Laser Scanning Microsystem (CLSM) is a very advanced analysis instrument with high precision. The author and her colleagues have discovered a new method for geological studies using the CLSM, especially for studies on fossils, minerals and rocks. They scanned the samples with transmitted or reflected light and got a series of images, then processed them with Boolean Logic, and contrasted and recombined three-dimensional views so that the structures inside and outside of the samples can be observed more clearlly. The new method is successful in solving the problems of geological samples lacking fluorescence, with dark colors and hard to create 3-D animations, enhancing the value of CLSM in geological studies and promoting the development of geological studies from macroscopic toward microcosmic ones.