We developed a novel infrared-assisted roll-to-roll embossing method which enables the rapid replication of microfeatures onto the surfaces of flexible polymer substrates. An infrared assisted roll-to-roll embossing facility was designed and built in our lab especially for this study. Metallic rollers bearing micropatterns of two different feature sizes, namely 150 um and 20 um in depth, were employed. During roller embossing, the infrared radiation shed on the rollers and the energy was converted into heat to melt the polymer substrates and to replicate the microstructures. The influence of various processing parameters on the replicability of microfeatures was investigated. Under the proper processing conditions, double-sided flexible polymer substrates with microstructures could be successfully fabricated. The proposed method shows great potential for fast fabrication of micro-optical components due to its simplicity and versatility.