This paper presents a microfluidic device with a nano-channel prepared by focused ion beam (FIB) milling for microbial cell lysis and nucleic acid extraction. The device prepared in a quartz slide combines two microchannels connected with one nanochannel in the middle with dimensions of 100 nm (width) and 250 nm (depth) and 1 μm (length). The capturing of a single or a few cells and their lysis for extraction of DNA in nanochannel were demonstrated. The purity and quantity of the extracted genetic material was tested using a UV spectrometer. The results revealed that the extraction methodology was successful and may be well-suited to integration in analytical lab-on-a-chip devices.