The construction of optical micro systems imposes new challenges on assembly technologies. These include the handling of multiple heterogeneous substrates, low thermal budget for the establishment of bonding connections, the accurate alignment of the substrates during wafer stacking and the integration of special components such as discrete optical lenses. In order to address these problems, a hierarchic wafer/component bonding process is proposed for the assembly of a 3-axis confocal scanning microscope. Experiment results indicate that the 9 constitutive components of the microscope, which are made from materials with different thermal expansion coefficients, can be joined together at less than 400°C global temperature. The strength of the achieved bonding is comparable to standard anodic or fusion bonding and can withstand diverse back-end-of-line processes such as dicing or grinding. Besides, the hermeticity of the developed bonding process is validated by monitoring the static deformation of a leak-indicating membrane.