In this paper, we have attempted to evaluate the depth of penetration of doxylated fatty acids in lipid vesicles and estimate the location of fluorophores in these model membrane systems. The fluorescence emission from the tryptophan residue in a transmembrane peptide is used as the fluorophore in this experiment, and fluorescence quenching results have been used to evaluate the depth of penetration of the doxylated fatty acids. Our results show that the peptides are partially bound to the surface of the membrane and the rest very likely are located with their tryptophan residues at the center of the bilayer. Detailed studies demonstrate that these doxylated fatty acid probes are efficient and excellent in locating the position of the tryptophan residues.