The molded interconnected devices (MID) technology is vastly growing as an important innovative technology in the field of electronics production. The laser direct structuring (LDS) method is one of the most common available technologies for building up MID’s products. The current existing knowledge in industry and in research about the standards in the respective manufacturing processes and process parameters is up to now not fully comprehensive in terms of mutual influencing and dependencies on each other. This is particularly the case for the three-dimensional applications and micro products. In the present contribution, a new simulation procedures based on a three-dimensional finite element model (FEM) has been developed. The effect of each of latent heat of fusion and temperature on the material properties as well as the 3D Gaussian heat source for the laser beam has been considered in this work. The used material was a polymer plate poly ether ether ketone (PEEK). The effect of the process parameters including laser power, speed, frequency, hatching percent or overlap between the laser lines, the laser incident angle, and the focal length have been investigated in experiments and simulations. The present simulation can be used to predict, temperature distribution, maximum temperature, groove dimensions, and groove profile at different process parameters setup. The theoretical and the experimental results can show a good accordance. It can be concluded that the FEM simulation can be used efficiently for predicating, analyzing, and optimizing the 2D/3D laser parameters for the LDS process.