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The lack of surface states within the bandgap of the perfect Si(100)2×1:H surface opens the way to scanning tunneling microscopy studies of dopant atom sites in Si(100). Both n- and p-type dopant-induced features were observed in filled- and empty-states images. The donor (arsenic)-induced feature looks as a protrusion in both the filled and empty states images, while the acceptor (boron)-induced feature appears as a hillock in the filled states image and a depression in the empty states image. The bias dependence, depth dependence, and dopant concentration dependence of the dopant-induced features were investigated in detail. Based on scattering theory, a numerical calculation was performed to achieve a fundamental understanding of these issues. The potential application of this study for three-dimensional dopant profiling with scanning tunneling microscopy on both p- and n-type samples is discussed, and the optimal scanning condition is also suggested. This technique may be a useful metric for characterizing dopant profiles in ultra-small electronic device structures.