The rapid development of biophotonics has advanced our understanding of the biological world through optical tools. On one hand, there is an increasing requirement to understand the heterogeneity of cells by precisely capturing and analyzing single cells. On the other hand, we have to develop biocompatible and implantable tools to explore the biological world. Although conventional optical tweezers have been widely used to immobilize single cells for further analysis, it has limitations, including manipulation inflexibility, use of bulky structures, diffraction limitations for nanoparticles, and limited trapping functions. We use a tapered optical fiber to realize optical trapping and manipulation with multiple functions and high flexibility, increased precision and high levels of integration. Both single particle/cell trapping for single cell analysis and multiple particle/cell assembly for biocompatible and implantable photonic devices construction have been realized. Using tapered optical fibers with different configurations, we achieved flexible trapping and controllable manipulation of different objects from microparticles to carbon nanotubes to single DNA molecules. Our tapered optical fiber-based single particle/cell trapping and multiple particle/cell assembly will advance our understanding of the biological world in a precise manner using biocompatible and implantable tools.