Carbon fiber technology drives significant development in lightweight and multifunctional applications. However, the microstructure of carbon fibers is not completely understood. A big challenge is to obtain the distribution of heteroatoms, for instance nitrogen, with high spatial resolution in three dimensions. Atom probe tomography (APT) has the potential to meet this challenge, but APT of carbon fibers is still relatively unexplored. We performed APT on three types of carbon fibers, including one high modulus type and two intermediate modulus types. Here, we present the methods to interpret the complex mass spectra of carbon fibers, enhance the mass resolution, and increase the obtained analysis volume. Finally, the origin of multiple hit events and possible methods to mitigate multiple hit events are also discussed. This paper provides guidance for future APT studies on carbon fibers, and thus leads the way to a deeper understanding of the microstructure, and consequently advancements in wide applications of carbon fibers.