The assembly of nanoparticles to form unique nanostructured materials is one of the most exciting areas due to their applications in various fields. There is a need to develop environment friendly routes to synthesize such nanomaterials with good control over the assembly of nanoparticles. In the current study, various template based methods have been developed to synthesize nanostructured materials using biologically safe approaches. In this context, natural and unmodified rhamnolipids were thermally self-assembled to form soft microtubules, which could act as a template to produce metal nanoparticles onto themselves due to the presence of rhamnose moieties at their surfaces. The porous gold/silver microwires like structures with fairly controlled nanofeatures were produced after calcination of rhamnolipids-nanoparticles composite fibers at high temperature. Moreover, rhamnolipids were used as reducing as well as stabilizing agent for the synthesis of highly stable gold and silver nanoparticles of fairly uniform size. In addition to the rhamnolipids, fungal hyphae were also used as living template to direct the organization of biocompatible gold nanoparticles, to form the fungal hyphae-gold nanoparticles composite materials. The calcination of these composites at high temperature led to the formation of porous gold microwire-like structures. The gold nanoparticles, used as building blocks, for this purpose were synthesized using tea extract as reducing and stabilizing agent. Such type of porous metal microwires might have potential applications in catalysis, sensors and Surface-enhanced Raman Spectroscopy (SERS). Template assisted highly porous metals (platinum, iron oxide) and hydroxyapatite were also prepared using polymer beads as sacrificial scaffolds. Two types of polymer templates, synthetic (polyacrylamide) and natural (calcium alginate), were used to direct the organization of metal and hydroxyapatite nanoparticles to produce organic- inorganic hybrid materials. Heat treatment of such composite materials at high temperature led to the formation of porous metals, metal oxide and hydroxyapatite materials. Moreover, the fungal biomass was incorporated inside the polymeric matrix of these beads to demonstrate the in situ synthesis of metal, especially gold and silver, nanoparticles. This provides a very simple and a straightforward strategy for the Abstract preparation of metal-polymer composite materials and ultimately porous metals after calcination. Different types of nanoparticles synthesized during present study were also evaluated to examine their role in affecting the polymerase chain reaction (PCR) efficiency. For that matter, an optimized PCR system, used for typing of Salmonella strains, was used to assess the effect of nanoparticles addition. In this study, three different types of nanoparticles were used such as citrate stabilized gold nanoparticles, rhamnolipids stabilized gold and silver nanoparticles and magnetic iron oxide nanoparticles. The elimination of non-specific amplification was somehow reduced while using gold and silver nanoparticles in appropriate concentration, but there was not much improvement in PCR efficiency in terms of yield. The surface chemistry of nanoparticles was found important for their effect on PCR. For example, citrate stabilized gold nanoparticles enhanced the PCR efficiency to some degree but rhamnolipid stabilized gold nanoparticles did not change the level of amplification of same target DNA. The magnetic nanoparticles, however, were found to inhibit the PCR under similar experimental conditions.