An integrated circuit structure includes a semiconductor substrate, and a FinFET over the semiconductor substrate. The FinFET includes a semiconductor fin; a gate dielectric on a top surface and sidewalls of the semiconductor fin; a gate electrode on the gate dielectric; and a source/drain region at an end of the semiconductor fin. A first pair of shallow trench isolation (STI) regions includes portions directly underlying portions of the source/drain regions, wherein the first pair of STI regions is separated by, and adjoining a semiconductor strip. The first pair of STI regions further has first top surfaces. A second pair of STI regions comprises portions directly underlying the gate electrode, wherein the second pair of STI regions is separated from each other by, and adjoining, the semiconductor strip. The second pair of STI regions has second top surfaces higher than the first top surfaces.