The use of plasma-polymerised fluoropolymer (CFxOy) thin films in the manufacture of microelectromechanical systems (MEMS) devices is well-established, being employed in the passivation step of the deep reactive ion etching (DRIE) process, for example. This paper presents an investigation of the effect of exposure to organic and aqueous liquid media on plasma-polymerised CFxOy thin films. Atomic force microscopy (AFM), scanning electron microscopy (SEM), ellipsometry, X-ray photoelectron spectroscopy (XPS) and dynamic wetting measurements were all employed as characterisation techniques. Highly basic aqueous solutions, including known silicon etchants, were found to cause delamination via degradation of the countersurface below the CFxOy thin film. Films were found to be stable in organic solvents, acidic aqueous solutions and slightly basic aqueous solutions.