Bioresorbable polymers such as poly(ε-caprolactone) (PCL) have a multitude of potential biomaterial applications such as controlled-release drug delivery and regenerative tissue engineering. For such biological applications, the fabrication of porous three-dimensional bioresorbable materials with tunable surface chemistry is critical to maximize their surface-to-volume ratio, mimic the extracellular matrix, and increase drug-loading capacity. Here, two different fluorocarbon (FC) precursors (octofluoropropane (C3F8) and hexafluoropropylene oxide (HFPO)) were used to deposit FC films on PCL scaffolds using plasma-enhanced chemical vapor deposition (PECVD). These two coating systems were chosen with the intent of modifying the scaffold surfaces to be bio-nonreactive while maintaining desirable bulk properties of the scaffold. X-ray photoelectron spectroscopy showed high-CF2 content films were deposited on both the exterior and interior of PCL scaffolds and that deposition behavior is PECVD system specific. Scanning electron microscopy data confirmed that FC film deposition yielded conformal rather than blanket coatings as the porous scaffold structure was maintained after plasma treatment. Treated scaffolds seeded with human dermal fibroblasts (HDF) demonstrate that the cells do not attach after 72 h and that the scaffolds are noncytotoxic to HDF. This work demonstrates conformal FC coatings can be deposited on 3D polymeric scaffolds using PECVD to fabricate 3D bio-nonreactive materials.