The patterning of sol-gel-derived thin films by micromolding in capillaries can produce unintended topographical deviations from the shape of the original mold that may limit the utility of the technique in potential applications. During drying and heat treatment, nonuniform shrinkage across the film due to the densification of the gel matrix results in “double-peak” film topographies whereby the film thickness is greater at the lateral edges than in the middle. Using the same framework used to understand the imbibition and wetting of the sol-gel in the capillary channels, we developed a mechanism to explain the formation of the double-peak profile. As a model system, patterned Pb(Zr_0.52Ti_0.48)O₃ thin films were studied. Atomic force microscopic characterization was used to quantify the effect of the rate of gelation on the topography of the patterned thin films. Modifications to the channel mold design eliminate the peak formation, producing more homogeneous patterns that better replicate the features of the mold.