Attractive interactions between molecules lead to formation of the liquid phase at sufficiently low temperatures. In the absence of external fields or containers, liquids assume the shape of spherical drops, which minimize their surface area. In systems with 3-D periodic boundary conditions (PBCs), which are routinely employed in molecular simulations, alternate configurations can be stable depending on the extent of the system. The stability of a variety of structures under 3-D PBCs originates from the underlying variation of free energy with density as shown elegantly by MacDowell and co-workers (MacDowell, L. G.; Shen, V. K.; Errington, J. R. J. Chem: Phys. 2006, 125, 3.). Here we present analysis of extensive Monte Carlo and molecular dynamics simulations of Lennard-Jones and water fluids to calculate free energy and explore the phase diagram that governs formation of different liquid assemblies. We also study metastability of different shapes and their interconversions by systematically initializing simulations in various configurations. Further, We present results on the rupture of thin liquid films on solid substrates, with focus on the evolution of liquid structure and the rupture mechanism. Our estimates of important capillary wavelengths from simulations are in good agreement with theoretical predictions of Vrij and Overbeek (Vrij, A.; Overbeek, J. T. J. Am. Chem. Soc. 1968, 90, 3074-3078.). Collectively, our work significantly extends the previous simulation studies of interfacial systems, and especially of thin-film structure, stability, and rupture processes in molecular simulations.