A method and apparatus for depositing a material layer to treat and condition a substrate, such as a fuel cell part, is described. The method includes depositing a hydrophilic material layer on a portion of the surface of the substrate in a process chamber from a mixture of precursors of the hydrophilic material layer. In addition, the method includes reducing a fluid contact angle of the substrate surface. The hydrophilic material layer comprises a wet etch rate of less than about 0.03 Å/min in the presence of about 10 ppm of hydrofluoric acid in water. The material layer can be used to condition various parts of a fuel cell useful in applications to generate electricity.