Atomic force microscopy is used to study the growth and annealing of Ge island.s on Si(100) by molecular beam epitaxy. The Ge island shape, size distribution, number density and spatial distribution under various growth conditions, such as different substrate temperatures, Ge beam fluxes, and annealing times, are investigated. By limiting the growth to a low coverage of 6 NIL of Ge, we find that either a low growth temperature (less than or equal to875 K) or a high beam flux can produce films dominated by pyramids of {105} facets. Domes of higher aspect ratios only appear at high growth temperatures or after a long time of annealing at low temperatures. This indicates that in the competition between the different kinetic processes responsible for the pyramid and dome formation, the domes require a higher activation energy and grow slower. We also demonstrate that appropriate annealing at low temperature can form locally ordered arrays of pyramids, with a narrow, size distribution.