The Integrated Systems Nanofabrication Cleanroom (ISNC) consists of 8,900 square feet of vertical-flow clean room space comprising 4 class 100 bays and 8 class 1,000 bays, 2 of which form a biology suite with its own dedicated air flow system. A full complement of utilities including high purity DI water, high purity nitrogen, reactive gases, chilled water etc. are available to each process bay. The ISNC integrates classic semiconductor tools and processes with biological, chemical, and medical substrates to extend beyond more traditional nano-device fabrication such as integrated circuits, quantum dots, single electron transistors, nanotips etc. toward DNA, single molecules, proteins and a host of other biologically relevant nanosystems. By proper process design and equipment selection, the ISNC provides the opportunity to successfully join standard process techniques with evolving bio-medical and nanoscale fabrication applications.