An embodiment is a semiconductor structure. The semiconductor structure comprises at least two gate structures on a substrate. The gate structures define a recess between the gate structures, and the recess is defined by a depth in a vertical direction. The depth is from a top surface of at least one of the gate structures to below a top surface of the substrate, and the depth extends in an isolation region in the substrate. The semiconductor structure further comprises a filler material in the recess. The filler material has a first thickness in the vertical direction. The semiconductor structure also comprises an inter-layer dielectric layer in the recess and over the filler material. The inter-layer dielectric layer has a second thickness in the vertical direction below the top surface of the at least one of the gate structures. The first thickness is greater than the second thickness.