The geometry of cutting flutes and the surfaces of end mills is one of the crucial parameters affecting the quality of the machining in the case of end milling. These are usually represented by two-dimensional models. This paper describes in detail the methodology to model the geometry of a flat end mill in terms of three-dimensional parameters. The geometric definition of the end mill is developed in terms of surface patches; flutes as helicoidal surfaces, the shank as a surface of revolution and the blending surfaces as bicubic Bezier and biparametric sweep surfaces. The proposed model defines the end mill in terms of three-dimensional rotational angles rather than the conventional two dimensional angles. To validate the methodology, the flat end milling cutter is directly rendered in OpenGL environment in terms of three-dimensional parameters. Further, an interface is developed that directly pulls the proposed three-dimensional model defined with the help of parametric equations into a commercial CAD modeling environment. This facilitates a wide range of downstream technological applications. The modeled tool is used for finite element simulations to study the cutting flutes under static and transient dynamic load conditions. The results of stress distribution (von mises stress), translational displacement and deformation are presented for static and transient dynamic analysis for the end mill cutter flute and its body. The method described in this paper offers a simple and intuitive way of generating high-quality end mill models for use in machining process simulations. It can be easily extended to generate other tools without relying on analytical or numerical formulations.