To reduce a thickness variation of a spin-on coating (SOC) layer that is applied over a plurality of first and second trenches with different pattern densities as a bottom layer in a photoresist stack, a two-step thermal treatment process is performed on the SOC layer. A first thermal treatment step in the two-step thermal treatment process is conducted at a first temperature below a cross-linking temperature of the SOC layer to cause flow of the SOC layer, and a second thermal treatment step in the two-step thermal treatment process is conducted at a second temperature to cause cross-linking of the SOC layer.