Methods for fabricating integrated circuits are provided. In one example, a method for fabricating an integrated circuit includes patterning a first photoresist layer overlying a mask blank that is mounted on a first chuck to form a first patterned photoresist layer. The mask blank is selectively etched using the first patterned photoresist layer to form a first patterned mask. The first patterned mask is mounted on a second chuck and a non-flatness compensation is determined. The first patterned mask is mounted on the first chuck and a second photoresist layer is patterned overlying the first patterned mask to form a second patterned photoresist layer. The second patterned photoresist layer includes a device pattern that has been adjusted using the non-flatness compensation. The first patterned mask is selectively etched using the second patterned photoresist layer to form a second patterned mask.