Ordered Au nanodisk arrays were fabricated on glass substrates using nanosphere lithography combined with a two-step reactive ion etching technique. The optical properties of these arrays were investigated both experimentally and theoretically. Specifically, the effects of disk diameter on localized surface plasmon resonance LSPR were characterized and compared with results from discrete dipole approximation DDA calculations. The effects of glass substrate, Cr interfacial layer, and Au thickness on LSPR were investigated computationally. Furthermore, thermal treatment was found to be essential in improving the nanodisk arrays' LSPR properties. Using atomic force microscopy and DDA calculations, it was established that the improvements in LSPR properties were due to thermally induced morphologic changes. Finally, microfluidic channels were integrated with the annealed disk arrays to study the sensitivity of LSPR to the change in surroundings' refractive index. The dependence of LSPR on surroundings' refractive index was measured and compared with calculated results. © 2008 American Institute of Physics.