An argon/hydrogen discharge plasma was created with a UHV compatible plasma source. This low energy plasma was utilized to remove – in a single step – the native oxide and the hydrocarbons from the wafer surface at substrate temperatures between 100°C and 400°C. During the plasma cleaning procedure, residual gas ions were monitored to elucidate the process chemistry. To optimize the procedure, the interfaces between the plasma cleaned wafer and the MBE grown epilayer were investigated by scanning electron microscopy (SEM) and cross-sectional transmission electron microscopy (XTEM). The cleaning process was also applied to patterned silicon substrates. Subsequent local epitaxial growth by MBE at 550°C without the typical high temperature annealing step was achieved, suggesting that the in–situ dry cleaning procedure caused no surface damage.