MEMS technology applying to the sensors and micro-electro devices is complete system. These microsystems are made by variable processes. Especially, the mentallization process has very important functions to transfer the power operating the sensor and signal induced from sensor part. But in the structures of MEMS the local stress concentration and deformation are often yielded by an irregular geometrical shape and different constraint. Therefore, this paper studies the effect of supporting type and thickness ratio about thin film of the substrate on the residual stress variation when the thermal loads is applied to the multi-layer thin film fabricated by metallization process. Specimens were made from several materials such as Al, Au and Cu. Then, uniform thermal load was applied, repeatedly. The residual stress was measured by FE Analysis and nano-indentation method using AFM. Generally, the specimen made of Al induced the larger residual stress than that of made of other materials. Specimen made of Cu and Au having the low thermal expansion coefficient induces the minimum residual stress. Similarly, the lowest indentation length was measured by nano-indentation method in the Si/Au/Cu specimen. Particularly, clusters are created in the specimen made of Cu by thermal load and the indentation length became increasingly large by cluster formation.