We use molecular dynamics (MD) to simulate an unstable homogeneous mixture of binary fluids (AB), confined in a slit pore of width $D$. The pore walls are assumed to be flat and structureless, and attract one component of the mixture (A) with the same strength. The pair-wise interactions between the particles is modeled by the Lennard-Jones potential, with symmetric parameters that lead to a miscibility gap in the bulk. In the thin-film geometry, an interesting interplay occurs between surface enrichment and phase separation. We study the evolution of a mixture with equal amounts of A and B, which is rendered unstable by a temperature quench. We find that A-rich surface enrichment layers form quickly during the early stages of the evolution, causing a depletion of A in the inner regions of the film. These surface-directed concentration profiles propagate from the walls towards the center of the film, resulting in a transient layered structure. This layered state breaks up into a columnar state, which is characterized by the lateral coarsening of cylindrical domains. The qualitative features of this process resemble results from previous studies of diffusive Ginzburg-Landau-type models [S.~K. Das, S. Puri, J. Horbach, and K. Binder, Phys. Rev. E {bf 72}, 061603 (2005)], but quantitative aspects differ markedly. The relation to spinodal decomposition in a strictly 2-$d$ geometry is also discussed.