In this work we present a finite element analysis of pyramidal and hut-shaped CoSi2 nanocrystals reactively deposited onto Si(001) substrates. These dots have been observed by us, as well as by other groups. Our analyses have yielded four major conclusions: (1) Elastic relaxation of CoSi2/Si mismatch strain by three-dimensional islands drives their nucleation, rendering flat, two-dimensional, layer energetically unfavourable. (2) The effect of the nanocrystal surface and interface energies for the observed vertical aspect ratios is negligible at small nanocrystal volumes. (3) Pyramids and huts with identical vertical aspect ratios are energetically degenerate. (4) Nanocrystal growth is only energetically favourable if accompanied by an increase in vertical aspect ratio. Most of these conclusions are consistent with those found in compressively strained layers, such as Si1−xGex layers on Si.