The morphology, topography and wetting with distilled water of Al–1.5 at. % Fe alloy films with a thickness 25–90 nm, formed on glass by ion-assisted deposition using a resonance ion source of vacuum electric arc plasma, have been studied. Using scanning probe microscopy, it is shown that, depending on the mode and the time of deposition, the modification of films is accompanied by changes in longitudinal and transverse roughness parameters, as well as parameters – dimensionless complexes, the measurement of which makes it possible to quantitatively describe the processes of coning in the Al–Fe alloy/glass system. Thus, the arithmetic mean roughness of the films increases with deposition time in the range 20–40 nm. Under self-irradiation conditions, a transition from island-like film growth to layer-by-layer film growth was detected. The influence of the substrate topography on the longitudinal step parameters of the film topography has been established. The size and surface density of the microdroplet fraction particles are studied by scanning electron microscopy. The frequency distributions of the microdroplet fraction by size are satisfactorily approximated by the lognormal distribution. It is found that in the mode of irradiation with intrinsic ions, 60–70% of the microparticles have a size of up to 0.8 μm. For the first time, a double Gaussian function was used to approximate the distribution histograms of local maxima and minima of the film relief, which made it possible to increase the accuracy of the description compared to the normal law. The effectiveness of this approach in analyzing the structure formation of nanometer films at various stages of growth has been demonstrated. Using the bi-Gaussian surface model, the role of topographic characteristics in controlling the wetting of modified coatings is revealed. The mechanism of heterogeneous wetting of hydrophilic films in the Cassie mode with contact angles ranging 50°–80° is discussed. It is found that in the potential mode, with an increase in the deposition duration to 10 h, the distribution of the film relief is close to the normal law, and the formation of a developed submicron conical morphology on the surface leads to blended wetting.