During the fabrication of nanopost arrays for measuring cellular forces, we have observed surface cracks in the negative molds used to replicate the arrays from a silicon master. These cracks become more numerous and severe with each replication such that repeated castings lead to arrays with missing or broken posts. This loss in pattern fidelity from the silicon master undermines the spatial resolution of the nanopost arrays in measuring cellular forces. We hypothesized that these cracks are formed because of a mismatch in the coefficient of thermal expansion (CTE) of PDMS and its oxidized surface layer. To study the fracture of PDMS due to thermal effects, we treated circular test samples of PDMS with oxidizing plasma and then heated them to cause surface cracks. These cracks were found to be more abundant at 180 °C than at lower temperatures. Finite element analysis of a bilayer material with a CTE mismatch was used to validate that thermal stresses are sufficient to overcome the fracture toughness of oxidized PDMS when heated to a curing temperature for PDMS. As a consequence, we have ascertained that elevated temperatures are a significant detriment to the reproducibility of nanoscale features in PDMS during replica molding.