Label free detection techniques such as surface plasmon resonance, carbon nanotubes, nanowires, and interferometry have been progressing rapidly for biosensing applications. Surface plasmon resonance is considered one of the most promising label free optical techniques. The use of nanohole arrays in a metal film allows for extraordinary transmission and has been motivated by their application as biosensors. Nanohole arrays present several advantages like smaller foot print, dense integration, lower limits of detection, and collinear optical detection. This thesis presents the design parameters for the optimization of sensitivity and resolution of nanohole arrays for refractive index sensing. A systematic study is provided of the influence of the nanohole array periodicity, diameter, and gold thickness. Focused ion beam was used to fabricate the nanohole arrays. A microfluidic device with a set of embedded nanohole arrays was developed and used to measure the sensing characteristics. The results are encouraging for potential future biosensing tests. / Graduate