A precise bonding technique, transmission laser bonding using energy transfer, for polymer micro devices is presented. The irradiated IR laser beam passes through the transparent part and absorbed on the opaque part. The absorbed energy is converted into heat and bonding takes place. In order to optimize the bonding quality, the temperature profile on the interface must be obtained. Using optical measurements of the both plates, the absorbed energy can be calculated. At the wavelength of 1100nm $87.5\%$ of incident laser energy was used for bonding process from the calculation. A heat transfer model was applied for obtaining the transient temperature profile. It was found that with the power of 29.5 mW, the interface begins to melt and bond each other in 3 sec and it is in a good agreement with experiment results. The transmission IR laser bonding has a potential in the local precise bonding in MEMS or Lab-on-a-chip applications.