The structural design of removable partial dentures (RPDs) is critical for preventing distortion of the prosthesis, protecting abutment teeth and residual ridges as well as for high masticatory performance. The aim of this study was to clarify the feasibility and utility of a computer-aided designing (CAD) system with finite element analysis (FEA) for molar teeth arrangement in unilateral distal extension base RPDs. The shapes of artificial teeth and residual ridge were measured and converted into point group data. Solid models were created from surface-modelled point group data in a 3D surface CAD format. An occlusal rim was created on the residual ridge mucosa and the occlusal rim - residual ridge mucosa model with FEA function was created. Stress distribution on the residual ridge mucosa was compared by changing the loading point. The artificial teeth were then arranged in locations with the lowest amount of stress. After building an artificial teeth - saddle - residual ridge mucosa model, stress distribution in the residual ridge mucosa was re-evaluated by simulating occlusal force. On the occlusal rim - residual ridge mucosa model, stress was reduced when the loading point was located around the buccal shelf where functional cusps of artificial teeth were charted. It was confirmed that stress distribution in the residual ridge mucosa was equalized on the artificial teeth - saddle - residual ridge mucosa model. This system might be clinically useful tool for designing RPDs if FEA-guided designing of retainers and connectors can be added.