The present paper describes a novel approach to interconnecting and assembling components of MEMS at room temperature. The main drawback of the conventional bonding methods is their rather high process temperatures. The new method, which is referred as the surface activated bonding (SAB), utilizes the phenomena of the adhesion between two atomically clean solid surfaces to enable the bonding at lower temperature or even at room temperature. In the bonding procedure, the surfaces to be bonded are merely brought into contact after sputter-cleaning by Ar fast atom in ultrahigh vacuum conditions. TEM observations of the bonded interfaces show that a direct bonding in atomic scale is achieved in the interface between the micro-components. Based on the concept of this new bonding technology, a micro-assembly system was developed. The micro-assembly system is operated by means of a virtual manipulation system in which 3D model of the micro-components are manipulated virtually in a computer graphics constructed in the world wide web (WWW) scheme. The micro-assembly system will provide a new design tool of three dimensional MEMS by combining the possibility of the flexible assembly and the intuitive operations.