Thin film coatings are ubiquitous in modern daily lives, from the semi-conductor industry to aesthetic applications, and rely on the modification of a given material to enhance its surface properties. At CERN (European Organization for Nuclear Research), thin film coatings are used for several applications related to the accelerator technology field, such as electron cloud mitigation, continuous pumping or radio-frequency (RF) superconductivity. This PhD thesis aims at studying the use of a Particle-in-Cell Monte Carlo/ Direct Simulation Monte Carlo (PICMC/DSMC) numerical code applied to the modelling of deposition processes. The present study focuses on niobium thin film deposition on copper RF cavities of peculiar geometries and large sizes. Numerical simulations can help to understand and improve process parameters in existing systems, and guide the design of future coating systems such that thin film characteristics can be predicted and expensive times of Research and Development can be reduced. In the first part of this thesis, critical parameters are identified to provide an accurate modelling of glow discharge plasmas commonly used in coating applications with the PICMC module of the numerical code. A dedicated experimental system is designed to enable both DC diode and DC magnetron operation with a coaxial cylindrical plasma source. Suitable ion-induced secondary electron emission yield and energy distribution are numerically assessed by matching simulated discharge voltages and currents with experimental ones. Simulated local plasma parameters, such as electron density and energy, are compared with experimental measurements obtained with a Langmuir probe. In the second part, transport simulations of sputtered neutral niobium atoms performed with the DSMC method are validated by comparing simulated deposition rates on a substrate with experimental ones with a compact hollow cathode magnetron sputtering source. At last, the validated ab initio methodology for coating process modelling, from plasma simulation and extraction of sputtering profiles to sputtered niobium atoms transport, is applied to typical coating systems used at CERN. The scalability of low discharge power simulation results to realistic powers is first demonstrated for a planar magnetron source in terms of cathode erosion and deposited thin film thickness profiles. Then, an elliptical RF cavity is used as a case study to apply the full methodology in a real substrate of complex shape. PICMC and DSMC simulation results are further extended towards thin film growth modelling, and simulated thin film morphology is compared with experimental Focused Ion Beam/Scanning Electron Microscopy imaging of the niobium layer.