3D Printing, also called Additive Manufacturing, has become a promising manufacturing method to produce parts in various fields as it can produce parts even with very irregular shapes in a relatively shorter process and time. However, during the printing process, some problems could decrease the accuracy and quality of the printed parts, such as warpage due to thermal strains, deformation due to inadequate supports, etc. The finite element method is most commonly adopted to evaluate engineering problems in advance to reduce possible failures; however, the element meshes, needed for analyses, are always irregularly distributed, especially for irregular objects, and cannot match the layer-by-layer growing shapes of the printed parts in the 3D printing process. Without a proper element mesh, the analysis cannot be performed. To overcome this problem, a layer-based mesh generator combined with a corresponding scheme for the 3D Printing simulation is proposed and developed. With the proposed methods, the analysis models can be designed and generated to match the growing shapes, i.e., layer-by-layer, and used to simulate the layer-by-layer growing behavior in the 3D printing process. Moreover, the proposed schemes directly adopt the Stereo-Lithography (STL) formatted geometric data as the geometry model on which the mesh generation and simulation are based. This makes them even easier to use since the STL geometry format is a De facto standard format used in the 3D printing industry. Several simulation cases have been conducted to demonstrate the effectiveness and efficiency of these proposed schemes.