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Nanoelectrode arrays (NEA) using 1-D nanomaterials as the electrode material have shown promise for biosensing applications. Vertical, freestanding, individual carbon nanofibers (CNFs) on patterned substrates constitute one example of NEA in the literature. The development of a biosensor system using this NEA first requires reliability studies prior to undertaking system integration with microfluidics and sample handling aspects. Here, we have investigated the effect of temperature and process conditions on the diameters and quality of the CNFs using atomic force microscopy (AFM). A Taguchi approach is employed to study the temperature effect in etched and unetched CNFs using AFM followed by a statistical analysis.