Fluorinated thin layers were created on CTMP sisal and filter paper surfaces by using pentafluorophenyldimethylsilane (PFPDMS) under RF-plasma conditions. Surface wettability and water absorption of unmodified and modified samples of both materials were evaluated through contact angle and Cobb test techniques, respectively. The mechanical strength and optical properties were also analyzed. The surface functional groups produced were evaluated using X-ray photoelectron spectroscopy, Electron Spectroscopy for Chemical Analysis (ESCA) and Attenuated Total Reflectance Fourier Transform infrared (ATR FT-IR) spectroscopy. Surface morphological changes after plasma treatment were evaluated using Scanning Electron Microscopy (SEM) and Atomic Force Microscopy (AFM). PFPDMS-plasma treatment of sisal CTMP reduced water absorption from more than 400 , and after PFPDMS-plasma treatment it was 134. Strength properties were slightly reduced in some cases and brightness was reduced in most of the trials, turning to yellow. ATR FT-IR and ESCA spectroscopy indicated a fluorinated aromatic surface, whereas AFM and SEM showed a smooth surface coating for both sisal and filter paper after PFPDMS-plasma treatment. A fully coated surface with a very high hydrophobic character was observed. This new property can be attributed to the formation of a crosslinked polymer network of covalently bound PFPDMS-based units on the paper surface as shown by the presence of CASi, CAOASi, CACF x , and CAF bonds.