Purpose Production of highly penetrable and targetable drug delivery particles is mainly focused by current therapy and such focus is achieved in our present study. The carbon nanoparticle (CNP) prepared from purely natural source was modified from spherical shape to cylindrical floral like structure after treatment with the anticancer drug methotrexate (CM). Methods The physiochemical properties of the CNP and CM was characterized using FT-IR/Raman Spectrometer, XRD, SEM, AFM, particle size analyzer and its biological evaluation using haemolysis and MTT assay. Results The shift in FT-IR peaks at 1592, 1120 cm(-1) and peaks of raman spectra observed at 1303, 1300 cm(-1) represents ordered carbon nanotubes. The morphological change from spherical to cylindrical floral like structure was observed using SEM and AFM and its particle size distribution analysis shows an average diameter of 269 nm for CM. XRD peak at 2 theta = 23.86A degrees (002) indicates the presence of large amount of amorphous material that corresponds to multi-walled carbon nanotubes. Haemocompatibility studies proved the safety level usage as 100 mu g/ml and MTT assay shows viability rate of 85-98% with mouse embryonic fibroblast (NIH/3 T3) and 30-45% with pancreatic carcinoma (MIA PaCa-2) and gastric cancer cell lines (SNU- 484) respectively.These results are also supported by phase contrast microscope images observed after staining with calcein AM and EthD-1. Conclusions The morphologically modified CNPs has shown good anticancer, biocompatibility and haemocompatibility property which is an important criterion to be satisfied by a biomedical product.