Atomic scale desorption and deposition of hydrogen (H) atoms on H-terminated Si(001) surfaces by a scanning tunneling microscope (STM) have been studied. Hydrogen atoms are extracted at either polarity of sample bias voltage. Desorption rate of H atoms shows a power-law dependence on tunnel current (I_t). When H atoms are locally extracted from a Si(001)-(3×1)-H surface, the dihydride rows partly disappear and instead new monohydride rows appear. Opposite local phase transition from 2×1 structure to 3×1 structure is also observed using H covered tips. Silver (Ag) growth on a pre-patterned Si(001)-(2×1)-H surface has been studied. An isolated dangling bond site can be occupied by an isolated single Ag atom or a 3-dimentional Ag cluster. On a wire of dangling bonds, Ag grows layer-by-layer along the wire.