Based on the original design of the confocal scanner system by Dr. Eisen and his colleagues at Stanford Univ., we have developed a modified confocal scanner system. The modified scanner only used one PMT instead of two PMTs in its precedent one. About half of the dichroic beamsplitters were replaced by reflection mirrors in the modified system. Therefore, we will be able to reduce the power of laser by a fact of 1.5. It will enhance the stability of the laser power and increase the accuracy of the detection system. The size of the modified system was decreased due to the simplified optics system. The optical system and the preliminary scanning results of this modified confocal scanner system will be presented in this paper. We will also discuss some possible further improvement of the system.