A simple method is proposed for the chemical modification of carbon nanotubes (CNT) thin film counter electrodes (CE) for the replacement of fluorine-doped tin oxide (FTO) and platinum catalyst (Pt) while retaining light transparency. In order to decrease the sheet resistance, CNT thin films underwent various concentrations (≤10 M) and durations of HNO3 treatment prior to cell fabrication, and the effect on thin film properties was analyzed. P-doping was observed, and the maximum change in work function was found to be +0.35 eV with 4 M HNO3. Optimum sheet resistance reduction (50%) and work function increment were achieved after 1 h treatment with 4 M HNO3. Changes in optical transmittances for all samples were negligible (± 5%). Pristine and HNO3 treated films on plastic substrates were tested as CE in flexible bifacial dye sensitized solar cells (DSSC). Most significant improvements in conversion efficiencies were obtained when CNT on plastic substrates were pretreated with 8 M HNO3 (from 1.18% to 1.40% under roomlight, from 0.19% to 0.26% under 1 Sun).