As the market changes at the increasingly rapid pace, the new products are developed quicker, the product cycles are shorter, and the production quantity is getting less. Great advantages are created as the new products are marketed faster with fewer designing errors and lower production costs. The Rapid Prototyping (RP) has been identified as one of the most potential techniques to deliver these advantages. However, the use of the RP systems is limited by the low product strength, the bad surface roughness and the high dimension errors. As this, this study focuses on optimizing the FDM process of the RP systems. The study on its early stage was based on the Taguchi method to establish the building factors of the rapid prototyping and the various levels of these factors. The ultimate tensile strength, the dimension accuracy and the surface roughness are analyzed. Through analysis of variance (ANOVA) and contribution approximation, the significant building factors of each quality feature and the feature combinations of each best quality feature are obtained. The following steps are setting weight for each quality feature of the previous Taguchi method, obtaining the estimated multiple building quality features through integrating the gray theory, and getting a set of the optimal building factors. Finally, the result is verified by the gray theory and the TOPSIS evaluation method. It is proved the optimal quality feature combinations of the multiple building factors can be obtained by integrating the gray theory and the Taguchi method. The result is further verified by the TOPSIS evaluation method, showing the model can get the multiple building quality features of the Rapid Prototyping.