To ensure that any proposed microstructure design fortifies the device from the stress due to load applied during and post fabrication process its structural modeling is mandatory. The work presented in this paper highlights the need to optimize the thin membranes or films for fabrication of thermoelectric microstructures. This paper analyses the stress and deformation in thin film due to suction load during photolithography (SUSS MicroTec Lithography) which exerts 0.8 bar pressure on the film. Investigation and characterization of 3 types of thermoelectric membrane designs are presented using Finite Element Method software COMSOL Multiphysics™ 3.3a at applied load of 80000 N/m2. These characterizations are significant for the stability and feasibility of structures during processing and thereafter. A membrane experiencing stress above 5e8 dynes/cm2 is considered stressed film for the thermoelectric membrane. However, a microstructure with stress below 5e8 dynes/cm2 is taken low stressed. The microstructure device sized 9.7 mm × 9.7 mm is optimized by doing comparison of stress and deformation observed in differently designed membranes of varying thickness and widths. For successful fabrication and operation of a device it is necessary that before moving to fabrication stage, the proposed micro-structure device must be analyzed and optimized by structural modeling to avoid any kind of undesirable deformation or ductile failure. © 2012 IFSA.