The instability, dynamics and morphological transitions of patterns in thin liquid films on periodic striped surfaces (consisting of alternating less and more wettable stripes) are investigated based on 3-D nonlinear simulations that account for the inter-site hydrodynamic and surface-energetic interactions. The film breakup is suppressed on some potentially destabilizing nonwettable sites when their spacing is below a characteristic lengthscale of the instability (λ h ), the upper bound for which is close to the spinodal lengthscale. The thin film pattern replicates the substrate surface energy pattern closely only when, (a) the periodicity of substrate pattern matches closely with the λ h , and (b) the stripe-width is within a range bounded by a lower critical length, below which no heterogeneous rupture occurs, and an upper transition length above which complex morphological features bearing little resemblance to the substrate pattern are formed. PACS numbers: 68.15.+e, 47.20.Ma, 47.54.+r, 68.08.De, 68.08.Bc Self-organization during dewetting of thin films on deliberately tailored chemically heterogeneous substrates is of increasing promise for engineering of desired nano-and micro-patterns in thin films by templeting [1,2,3,4,5,6,7,8,9,10,11]. On a chemically heterogeneous substrate, dewetting is driven by the spatial gradient of micro-scale wettability [12], rather than by the non-wettability of the substrate itself. The latter occurs in the so called spinodal dewetting on homogeneous surfaces [13,14]. While the rupture of a thin film on a single heterogeneous patch is now well understood, patterned substrates pack a large density of surface features that are closely spaced. How does hydrodynamic interactions between the neighboring heterogeneities affect the pattern evolution dynamics and morphology in thin films? This question, which is addressed here, is central to our understanding of how faithfully the substrate patterns are reproduced in a thin film spontaneously, i.e., how effective is the templeting of soft materials by dewetting route and what are the conditions for ideal templeting? An associated question for both the patterned and naturally occurring heterogeneous surfaces is whether all the potentially dewetting sites remain active or "live" in producing rupture when they are in close proximity. These questions are resolved based on 3-D nonlinear simulations of the stability, dynamics and morphology of thin films on periodic chemically heterogeneous surfaces.The substrate considered consists of alternating less wettable and more wettable (or completely wettable) stripes that differ in their interactions with the overlying film. The key parameters of the substrate pattern are its periodicity interval (center-to-center distance between two consecutive stripes, L p ) and the length-scale of the less wettable stripe (stripe-width, W ). The following nondimensional thin film equation governs the stability and spatio-temporal evolution of a thin film system subjected to the excess intermolecular in...