Silicon-to-silicon fusion (or direct) pre-bonding is an important enabling technology for many emerging microelectronics and MEMS technologies. A silicon-silicon direct bond can be easily formed, where the wafer surfaces are highly flat and very clean (Tong and Gosele), however for practical structured MEMS devices, wafer bow and local roughness may be compromised such that it is no longer a trivial task to achieve a direct bond. Tooling has been developed to facilitate the in situ alignment and bonding of silicon-to-silicon wafers in a vacuum chamber. The rate and direction of the bond propagation are controlled, thus minimising the occurrence of non-particle related voids. The tooling system also allows wafers with "non-ideal" surfaces or warped profiles to be bonded, by maximising the area across which bonding occurs and providing in situ annealing. The ability to anneal the wafers while maintaining clamping force creates attractive forces high enough to overcome the mechanical repulsive forces between the wafers and maintain a permanent bond. The tooling system can also be configured to give control over the bow or residual stress in the bonded pair, a factor that is critical in multi-stack direct wafer bonding.