Surface directed instability and dewetting in thin films and resulting morphologies are studied using 3D nonlinear simulations based on the equations of motion, both for the isotropic and anisotropic 2D substrate patterns. Three different substrate (wettability) patterns are considered: (a) arrays of more (or completely) wettable rectangular blocks on a less wettable substrate, (b) arrays of less wettable blocks on a more (or completely) wettable substrate, and (c) a checkerboard pattern of alternating more and less wettable blocks. An ideal replication of the surface energy pattern produces an ordered 2D array of liquid columns (in case 1), or a matrix of holes on a flat liquid sheet (in case 2), or a checkerboard pattern of alternating liquid columns and holes/depressions (in case 3). The effects of pattern periodicity, domain widths, anisotropy, and wettability on the morphological phase transitions are presented. Regardless of the precise geometry of the substrate pattern, templating is found to be better on a completely wettable substrate containing the less wettable blocks, rather than on a less wettable substrate having more wettable blocks. Complete wettability (zero contact angle at all thicknesses), of either the blocks or their surroundings, ensures the pinning of the liquid contact line at the block boundaries. Thus, complete wettability leads to better templating compared to partially wettable substrates. Ideal templating is found possible only when the following conditions are met: (a) the periodicity (L-px and L-py) of the pattern is more than lambda(h); where lambda(h) is a characteristic length scale found to be close to the spinodal length scale of the less wettable part, lambda(m), (b) the less wettable area fraction, A(f), should be less than a transition value beyond which the liquid spills over the less wettable part leading to a morphological transition from discrete columnar structure to continuous liquid ridges, (c) less wettable block/channel width should be less than a transition length scale (similar to0.5lambdam), and (d) the aspect ratio of the periodicity intervals (L-px/L-py) should be close to 1. Anisotropy in the substrate periodicity leads to stripe-like liquid patterns whenever either L-px or L-py is less than lambda(h). Large values of periodicity lead to the formation of novel "block mountain-rift valley" or "flower" like microstructures that do not replicate the substrate energy pattern. Interestingly, the near ideal templating of more complex substrate patterns, e.g., alphabets, is also guided by the above conditions.