Thermal reflow is an important property for thermoplastic polymers, which has been studied extensively especially for photoresists and electron beam resists in semiconductor industries. While the surface smoothening effect is beneficial to reduce the roughness of micro- and nanostructures, the drastic morphology change has been tested to be efficient to fabricate optical devices like microlens arrays. Plasma-polymerized fluorocarbon (PPFC) is a feasible polymer material, which can be achieved conveniently with standard plasma etching systems, however, there have been limited studies regarding its properties and applications apart from its usage as a passivation layer during reactive ion etching. In this study, the thermal reflow behavior of PPFC on various substrates will be presented, including planar surfaces, gratings and trenches. Importantly, the formation of buried micro- and nanochannels has been demonstrated, when PPFC is heated above its glass transition temperature on trench structures. This encapsulation dynamics is analyzed with regard to various parameters like temperature and duration of thermal treatment, trench widths and initial thickness of PPFC film. As a proof of concept, silicon nanorods have been encapsulated in the microchannels by the reflowed PPFC. The results have demonstrated strong potentials of PPFC for applications like micro- and nanofluidics, microcontainers and drug delivery. Because of its good chemical stability and biocompatibility, PPFC can also be expected to be used for various biological devices like brain-machine interfaces, neural probes, epidermal devices and biological implants.