We present a set of practical rules critical for designing and building a modern nanotechnology laboratory, focused on photonic applications in a cleanroom environment. We show the impacts on time, cost and quality of early design decisions and its importance on achieving the final fully functional laboratory. Best practice examples are presented for setting up a modern laboratory/facility, following analysis of the time, cost and quality constraints. The case study presented is the engineering and architectural solution of the nanofabrication cleanroom facility in the Advanced Technology Centre at Swinburne University of Technology, Australia. Set of practical rules is established for the cost and time efficient set up of the nanotechnology facilities for the research and development.© (2011) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.