This paper reports on the recent work carried out as part of the EU funded NanoMend project. The project seeks to develop integrated process inspection, cleaning, repair and control systems for nano-scale thin films on large area substrates. In the present study flexible photovoltaic films have been the substrate of interest. Flexible PV films are the subject of significant development at present and the latest films have efficiencies at or beyond the level of Si based rigid PV modules. These flexible devices are fabricated on polymer film by the repeated deposition, and patterning, of thin layer materials using roll-to-roll processes, where the whole film is approximately 3um thick prior to encapsulation. Whilst flexible films offer significant advantages in terms of mass and the possibility of building integration (BIPV) they are at present susceptible to long term environmental degradation as a result of water vapor transmission through the barrier layers to the CIGS (Copper Indium Gallium Selenide CuInxGa(1-x)Se2) PV cells thus causing electrical shorts and efficiency drops. Environmental protection of the GIGS cell is provided by a thin (40nm) barrier coating of Al2O3. The highly conformal aluminium oxide barrier layer is produced by atomic layer deposition (ALD) where, the ultra-thin Al2O3 layer is deposited onto polymer thin films before these films encapsulate the PV cell. The surface of the starting polymer film must be of very high quality in order to avoid creating defects in the device layers. Since these defects reduce manufacturing yield, in order to prevent them, a further thin polymer coating (planarization layer) is generally applied to the polymer film prior to deposition. The presence of surface irregularities on the uncoated film can create defects within the nanometre-scale, aluminium oxide, barrier layer and these are measured and characterised. This paper begins by reporting the results of early stage measurements conducted to characterise the uncoated and coated polymer film surface topography using feature parameter analysis. The measurements are carried out using a Taylor Hobson Coherence Correlation Interferometer an optical microscope and SEM. Feature parameter analysis allows the efficient separation of small insignificant defects from large defects. The presence of both large and insignificant defects is then correlated with the water vapour transmission rate as measured on representative sets of films using at standard MOCON test. The paper finishes by drawing conclusions based on analysis of WVTR and defect size, where it is postulated that small numbers of large defects play a significant role in higher levels of WVTR.