One embodiment of the present invention provides a system for bonding a first substrate and a second substrate. During operation, the system starts by treating a first surface of the first substrate and a second surface of the second substrate with a hydrophilic treatment. The system then transfers a first oligomer layer onto the treated first surface and a second oligomer layer onto the treated second surface. Next, the system treats the first oligomer layer and the second oligomer layer for hydrophilic activation. The system subsequently brings the first oligomer layer into contact with the second oligomer layer, thereby allowing the two oligomer layers to adhere and form a single bonding layer between the first substrate and the second substrate. In particular, each of the first oligomer layer and the second oligomer layer is a polydimethylsiloxane (PDMS) layer.