The interaction between an AFM probe and a thin water film deposited over a flat substrate is studied using Molecular Dynamics (MD). The effects of the film thickness and of the probe radius on both the deformation height of the liquid interface, and the distance of the jump to contact at which the liquid comes in direct contact with the probe, are investigated. The dynamics of the surface deformation and the role of interface fluctuations are studied in details. The systems considered belong to the thin film regime described in a semi-analytical model previously established by Ledesma et al. (Langmuir 2013, 29, 7749-7757). MD simulations predict that for shallow films, both the distance at which the jump to contact occurs, and the surface maximal deformation height increase steadily with the layer thickness regardless of the probe radius, which is in agreement with the theoretical model proposed. The results also reveal that the deformation of the interface is localized under the probe apex, and that it is highly subject to fluctuations which result in an instability of the deformation for the considered systems. The molecular approach hence points out the importance of fluctuations when it comes to the description of nanosystems involving soft interfaces. This unveils the needs for the establishment of thermal models to improve accuracy.