Microstructured polydimethylsiloxane (PDMS) is an important and widely used material in biology and chemistry. Here we report that micrometer- and nanometer-scale features can be introduced into the surface of PDMS in a process that is functionally equivalent to embossing. We show that surface features <50 nm can be replicated onto the surface of previously cured PDMS at room temperature and at low pressure. This type of embossing can be performed on samples in solution. It also allows one template to be used for many different types of microstructures by changing the embossing time or serial embossing at different alignments. The balance between elastic and plastic properties of the PDMS has the effect of high-pass filtering the features that are captured and produces a sample that is suitable for sensitive surface characterization technologies such as atomic force microscopy. These findings extend the applications of PDMS as well as open the possibility for new uses.