Thermal, deformation, and optical simulations are performed on polymer PMMA waveguide at different temperatures by using FEM (Finite Element Method). The models which are used in the simulations aim to calculate the heat distribution and thermally induced mechanical stress. The microheater is implemented at the top of the waveguide and inside the top cladding to analyze the thermo-optic effect on the waveguide. We found that the microheater is more effective and causes a uniform thermal distribution in the core. Also, this thermal effect results in a change of refractive index which is analyzed in this paper. It is found that the mechanical stress on the waveguide affects the shape and the index of refraction of the waveguide. Hence, it plays a role in the optical performance. Shear stress has little effect on the waveguide along the propagation axis, because we fixed the waveguide from the sides.