Soft lithography was used to replicate nanoscale features made using electron beam lithography on a polymethylmethacrylate (PMMA) master. The PMMA masters were exposed to fluorinated silane vapors to passivate its surfaces so that polydimethylsiloxane (PDMS) did not permanently bond to the master. From scanning electron microscopy, the silanization process was found to deposit a coating on the master that was a few hundreds of nanometers thick. These silane films partially concealed the nanoscale holes on the PMMA master, causing the soft lithography process to produce PDMS features with dimensions that were significantly reduced. The thickness of the silane films was directly measured on silicon or PMMA masters and was found to increase with exposure time to silane vapors. These findings indicate that the thickness of the silane coatings is a critical parameter when using soft lithography to replicate nanoscale features, and caution should be taken on how long a master is exposed to silane vapors.