A three-dimensional (3D) integrated circuit (IC) includes a first IC and a second IC. The first IC includes a MEMS device and a first bonding structure. The second IC includes a second bonding structure. The first and second bonding structures are bonded together to couple the first IC to the second IC. A conformal barrier layer is disposed over a surface of the second IC nearest the first IC. An etch isolation structure is arranged beneath the surface of the second IC and encloses a sacrificial region which is arranged on either side of the second bonding structure and which is arranged in the second IC.