(001) n-type Ge has been implanted at given fluence and intermediate temperature with hydrogen ions using two processes: conventional in-line implantation and plasma based ion implantation. The as-created microstructure has been compared using transmission electron microscopy. In particular, it has been shown that the major differences observed are due to the implantation temperature, much higher during the PBII process. This suggests that plasma based ion implantation could be used for layer transfer in spite of a higher surface roughness observed after the PBII process.