Polymer solar cells (PSC's) have received much attention as a promising clean and green energy technology and the power conversion efficiency have steadily increased. There are several ways to improve the device efficiency of PSC, such as changing the active layer, insertion of the electron transport layer and the anode buffer layer. Among the several anode buffer layer materials, Poly(3,4-Ethylenedioxythiophene):Poly(styrene sulfonate) (PEDOT:PSS) is widely used as anode buffer layer due to its high transparency in the visible region, high thermal stability and mechanical flexibility. However, PEDOT:PSS suffers a problem of low conductivity and limits the device application. In this report, we present the preparation of PEDOT:PSS hole transport layer through a secondary doping with flouro compounds such as hexafluoroacetone (HFA) and hexafluoroisoproponal (HIPA) with various concentrations by spin coating technique. High performance of the hole transport layer is attributed to preferential phase segregation of PEDOT:PSS with HFA and HIPA solvent mixture treatment method. The improved performance of PSC was dependent on the structure of organic solvents and the concentration of flouro compounds in PEDOT:PSS solution. Using these optimized buffer layer, conjugated polymer solar cells with a Poly9-(1-octylnonyl)-9H-carbazole-2,7-diyl]-2,5-thiophenediyl-2,1,3- benzothiadiazole-4,7-diyl-2,5 thiophenediyl] polymer:[6,6]-phenyl-C71-butyric acid methyl esters (PCDTBT:PC71BM) bulk heterojunction have been produced. A detailed analysis of the surface morphology and optical studies are presented. The obtained results show that PEDOT:PSS optimized with HFA and HIPA organic solvents can be a very promising candidate for transparent anode buffer layer in the low cost organic solar cell devices. © 2013 SPIE.