According to the high accuracy of semiconductor equipments, PCB substrate with much thin thickness is required. However, it is very difficult to sustain the PCB substrate without deformation in case of horizontal installation, due to low bending stiffness. In this research, new PCB process equipment with vertical installation has been developed in order to solve the problem of PCB substrate damage during etching process. As the main parts of etching system on PCB substrate, PCB substrate and JIG are analyzed through finite element method and experimental test. Through the analysis results of stress state, we could find the optimal JIG design to make the damage as low as possible.