Carbon nanotubes (CNTs) due to their unique electrical, thermal, chemical and mechanical properties have been extensively studied in terms of both fundamental and practical applications such as electronics, energy storage, catalysis, fuel cells, solar cells, molecular separation, sensors, biosensors, drug delivery. The diameter and morphology of CNT is determined to be a key factor to govern the properties of CNT and extensive research has been directed to the growth of CNT structures with controllable dimensions. The presence of additional doping elements into CNT structure including nitrogen, boron, phosphor also can considerable alter their conductivity, chemical and biocombatibility properties. In this work, we present several synthetic approaches to prepare multi-walled carbon nanotubes (MWCNT) with controlled dimensions and chemically doped with selected elements (N and P). Our method is based on chemical vapour deposition (CVD) using nanoporous anodic alumina oxide (AAO) as template. The advantages of this process are because it is catalyst-free and dimensions of CNT structures are controllable by the template. The synthesis of CNT inside of pores of AAO template was performed in a custom designed CVD system using toluene/ethanol mixture as carbon precursors. To prepare CNT doped with nitrogen and phosphor several carbon precursors including ammonium, pyridine, melamine and triphenyl-phosphine were explored with aim to considerably improve their biocompatibility for biomedical application. Prepared CNT were liberated from AAO template are characterised by scanning electron microscopy (SEM), high resolution transmission electron microscopy (HRTEM), Raman spectroscopy, x-ray electron spectroscopy (XPS), x-ray powder diffraction spectroscopy (XRD and thermogravimetric analysis (TGA).