A method includes providing a first clock tree including a root clock and a plurality of levels of integrated clock gates (ICGs) under the root clock. The plurality of levels of ICGs in the first clock tree is flattened to generate a second clock tree including a plurality of ICGs in a same level under the root clock. A fake module is formed to reserve a region between the root clock and the plurality of ICGs. The fake module includes the root clock as a first input, and a first plurality of outputs coupled to clock-inputs of the plurality of ICGs. A skew balancing is performed on the second clock tree using a clock tree synthesis (CTS) tool to generate a third clock tree, wherein no buffers are inserted into the fake module, and wherein buffers are inserted by the CTS tool under the plurality of ICGs.