A conducting polymer of polypyrrole (PPy) has attracted lots of engineering interest for their potential applications in electrical devices. In this study, various fabrication methods of polypyrrole were investigated such as nanoparticle formation through microemulsion technique and surface deposition using chemically modified pyrrole monomer. When preparing PPy nanoparticles, the aggregation and electrical conductivity of PPy nanoparticles were influenced by both the surfactant type and reaction sequence. Electrical charge of surfactant influenced on the morphology and aggregation. The anionic surfactant resulted in large aggregates which is likely to be driven by doping of surfactant to the PPy backbone during polymerization. After the PPy nanoparticle formation, the prepared PPy nanoparticles were deposited on the substrate in couple of ways. Firstly, the PPy nanoparticles were bound to the silicon substrate using designer peptide with high affinity to PPy. Secondly, the pyrrole monomer was modified to directly react with substrate surface. Subsequently, the PPy nanoparitcle layer formation was achieved by chemical oxidation method. This study would provide an insight for the origin of PPy nanoparticle aggregation and innovative methods to fabricate PPy nanoparticles for the future use in electrical devices.