The main objective of this research is to reconstruct 3D rapid prototyping (RP) models for computer tomography (CT) medical images in fused deposition modeling (FDM). It demonstrates a technique to convert medical images to points cloud, and simplify into STL (Stereo-Lithography) triangular meshes for RP machine in fused deposition modelling. The grey prediction algorithm is used to sort contour point data in each layer of the medical image. The contour difference detection operation is used to sequence the points for each layer. The 3D STL meshes are then constructed by layer-by-layer sequence meshes algorithm to build the STL file. Once this STL file is saved, a 3D physical model of the medical image can be fabricated by FDM RP manufacturing, and its virtual reality model can also be presented for visualization. CT images of a human skull and femur bone were used as the case studies for the construction of the 3D solid model with medical images. The STL models generated using this new methodology compared to commercial computer-aided design (CAD) models. The results of this research are therefore clinically reliable in reconstructing 3D STL models for CT medical images.