Carbon materials find application in numerous fields because of its large specific surface area, good electronic conductivity, inexpensive and inertness under corrosive conditions. These materials on appropriate pre-treatment have shown to give better performance which is attributed to different functional groups on surface. Surface functionalization, apart from showing improved performance also impact structure and charge carrier concentration of carbon materials and as we move towards large scale production there is a need to understand effect of these pretreatments to envision long term effects on device performance to minimize losses. We attempted to study, structural changes because of functionalization of carbon paper. Carbon paper electrodes are used widely for various electrochemical applications such as flow batteries, catalyst support in fuel cells, waste water treatment, Bioelectrochemistry. We employed Raman spectroscopy technique to study defects on carbon paper before and after functionalization and effect of these functionalization on charge carrier concentration. Carbon papers, pretreated employing different methods to study its effect on fibre structure in terms of defects and charge carrier distribution. This study could assist us to gain an important understanding on impact of conventional pretreatment methods being currently followed which is not ideal. This conventional pretreatment was also compared with nitrogen functionalization treatment which showed superior catalytic activity and a promising pretreatment method for large scale application.