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The paper describes a method to differentiate the VEP signals based on frequency domain analysis as normal (N), optic neuropathy (ON) and non-recordable (NR) groups for prognostic and therapeutic reasons. The frequency domain analysis provides valuable information on the overall composition of the VEP signal for all the three groups by time domain parameters of P100, latency and its peak. The spectrum of the VEP signal for all the three groups is calculated and various spectral parameters are extracted. Total power in the spectrum (TPS), mean power (MP) and summation of the frequency and the corresponding power products (SEPP) are the features extracted from the spectrum. Regression analysis is performed to establish a relationship between the means of the extracted feature and the three groups. A good correlation (r=-0.91 to -0.96) is observed with p< 0.05 for TPS, MP and SFPP for all the three groups. Follow-up VEP studies have been carried out to monitor the progress of optic neuropathy disease and therapeutic response to the treatment. One of the spectral parameter, TPS is used a quantification features to monitor the therapeutic response to the treatment for a case study in optic neuropathy. After medication a fifty percent improvement in TPS value is observed. Therefore TPS is an important features that can be used to quantify the recovery status of optic neuropathy subjects.