An alternative method is developed to remove metal from a work piece by combining a digital lithography system with biomachining. The purpose of this system is to obtain extra advantages as compared to conventional micro-fabrication processes currently used in practice. The use of microorganisms as a cutting tool in biomachining can eliminate the use of hazardous chemical materials, and the target surface is not affected by heat as a result of machining. The proposed process has a low material removal rate, but with less energy consumption. The greatest advantage is that the tools used in biomachining can be cultured continuously; i.e., they are renewable. Theoretically, the resolution of biomachining can reach 1 um due to the size of the bacteria. To achieve selective material removal, we combine the biomachining process with a polymer mask generated by a digital lithography (DL) system. In order to minimize errors and noise, the DL system was constructed by choosing robust and commonly available devices for most of the sub-tasks. This construction then can bring projected image onto work piece surface on fully controlled.