This study has addressed the effect of starting surface topography on the nucleation and growth of epitaxial siicide layers. CoSi2 layers were grown via the template technique on one-dimensionally patterned Si (100) substrates. These substrates contained mesa stripes, running parallel to Si, and exhibited either smoothly varying sinusoidal profiles, or a number of well defined Si Ihkl) facets. Conventional plan view and high resolution cross section transmission electron microscopy were used to analyze the films grown on these substrates. The orientation and morphology of the CoSi2 grains depend on the angle (θ), between the CoSi2 / Si interface normal and Si (100). High quality (100) oriented CoSi2 grew on the tops and bottoms of mesa structures, where θ < 5°, and formed atomically sharp interfaces with the substrate. In contrast, CoSi2 (110) and CoSi2 (221 ) grains nucleated along the sidewalls of the mesa structures. The CoSi2 (110) grains formed rough interfaces with the substrate and were terminated by regions of step bunching at the grain boundary / substrate triple points. CoSi2 (110) grains were most highly concentrated in regions where θ varied from 5° to 12°. Similarly, the CoSi2 (221 ) grains formed faceted (111) b-type silicide / substrate interfaces, and were most highly concentrated in regions where θ > 10°. These data suggest that double height steps, step bunches and facets on the substrate are related to the nucleation of misoriented silicide grains.