Methods of forming coplanar active regions and isolation regions and structures thereof are disclosed. One embodiment includes shallow-trench-isolation (STI) formation in a semiconductor-on-insulator (SOI) layer on a substrate of a semiconductor structure; and bonding a handle wafer to the STI and SOI layer to form an intermediate structure. The intermediate structure may have a single layer including at least one STI region and at least one SOI region therein disposed between the damaged substrate and the handle wafer. The method may also include cleaving the hydrogen implanted substrate and removing any residual substrate to expose a surface of the at least one STI region and a surface of the at least one SOI region. The exposed surface of the at least one STI region forms an isolation region and the exposed surface of the at least one SOI region forms an active region, which are coplanar to each other.