Surface roughening and defect formation of (100) Si at low temperatures during electron cyclotron resonance hydrogen plasma cleaning are studied in an ultrahigh vacuum environment, and a new model is proposed to explain their mechanisms. The effect of process parameters on surface roughness is quantitatively analyzed by atomic force microscopy and reflection high energy electron diffraction. Crystalline defect morphology is studied by transmission electron microscopy to understand its role in surface roughness. Surface roughness is strongly related to {111} platelet defects at the Si subsurface region and subsequent preferential etching at positions where {111} platelet defects intersect the Si surface. The formation of {111} platelet defects is determined by the subsurface hydrogen concentration, which is determined by incident hydrogen flux and substrate temperature. The preferential nucleation of etching reactions on the {111} platelet may be explained by the classical nucleation theory. Hydrogen ion flux and substrate temperature can be controlled successfully to tailor {111} platelet defect formation and hence, surface roughness.