The initial stages of growth of Si(100) epilayers were investigated using tapping mode-atomic force microscopy (TM-AFM). The epilayers were grown from silane at low temperatures (less than or equal to 700 degrees C) in a UHV-CVD system, after the Si(100) substrates were given an HF dip as the last cleaning step. Depending on the growth pressure, two basic surface morphologies can be identified at 650 degrees C. After an incubation period, high pressure deposition (typically 2 mTorr) results in very smooth layers. In contrast, layers grown at lower pressures (typically 0.2 mTorr) rapidly develop a rough surface morphology which consists of [110] oriented pyramidal pits. The incubation time, as well as the rough morphology are both attributed to C contamination. The growth temperature is also shown to affect the occurrence of the smooth or rough morphology. The resulting surface morphology is finally discussed by considering the steady state hydrogen coverage that exists on the surface during deposition.