Interstellar (IS) absorption lines or diffuse bands are usually extracted from early-type star spectra because they are characterized by smooth continua. However, this introduces a strong limitation on the number of available targets, and reduces potential studies of the IS matter and the use of absorptions for cloud mapping. We have developed a new and automated fitting method appropriate to interstellar (IS) absorptions in the spectra of cool stars that possess stellar atmospheric parameters. We applied this method to the extraction of three diffuse interstellar bands (DIBs) in high resolution VLT FLAMES/GIRAFFE spectra of red-clump stars from the bulge. By combining all stellar synthetic spectra, HITRAN-LBLRTM atmospheric transmission spectra and diffuse band empirical absorption profiles, we determined the 6196.0, 6204.5, and 6283.8{AA} DIB strength toward the 219 target stars and discuss the sources of uncertainties. To test the sensitivity of the DIB extraction, we compared all three results and compared the DIB equivalent widths (EWs) with the reddening derived from an independent extinction map based on OGLE photometric data. We also derived the three independent color excess estimates based on the DIB strengths and average linear correlation coefficients previously established in the solar neighborhood and compared with the OGLE photometric results.