We demonstrated that bacterial cells can be used as a mask material for microfabrication of GaAs and Si by a Cl2 inductively coupled plasma (ICP) etching process. The etching rate of Escherichia coli cells was similar to that of electron beam resist or nanoimprint resist. We also demonstrated the degradation of bacterial cells by low-pressure plasma treatment using O2, Ar, air, and H2O for removal of bacterial cells as the etching mask material. Bacterial cells were efficiently degraded by ions in the low-pressure discharge plasma. The proposed process using bacterial cells can be expected to be applied to semiconductor dry etching processes.