One of the major goals of experimental biology today is the visualization of biological processes down to the molecular scale in vitro or in vivo. In order to investigate these length scales, a number of probes have been developed, including organic dyes, fluorescent quantum dots and hybrid fluorescent nanoparticles. We have developed a class of hybrid fluorescent nanoparticles known as C dots based on the covalent incorporation of organic dyes into silica matrices. These particles can be synthesized in a variety of architectures suitable to many different biological tasks. In particular, we will discuss the use of core-shell nanoparticles for labeling cellular material in vitro, as well as core-functional shell particles for quantitative chemical sensing.