Laser ablation of mixed targets of 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA) with cobalt powder (PTCDA-Co) was carried out using the third harmonic of a Nd:YAG laser (355 nm) in order to prepare nanoparticles consisting basically of polyperinaphthalene (PPN), a member of the low dimensional graphite family. The optimized content ratio of Co to PTCDA (Co:PTCDA) for effective elimination reaction of anhydride groups of PTCDA was determined. We found that the ablation at Co:PTCDA of 4:1 and 8:1 enabled us to eliminate the side groups effectively. Furthermore, surface enhanced Raman spectroscopy with a tip of an atomic force microscope was carried out to investigate the molecular structure of each nanoparticle. Amplification of the Raman intensity by more than 100 times compared with conventional micro Raman spectroscopy was achieved by tip enhancement. A nanoparticle having a diameter of approximately 70 nm prepared by this method was found to possess PPN structure.