With the advancement of high throughput and high resolution volumetric brain imaging, there is an unmet need to trace dense neuron fibers and study long-range neuron connectivity. An initial pipeline is described for processing cellular-level neuronal fiber data acquired by a new super resolution imaging method called Magnified Analysis of the Proteome (MAP). First, a multiscale vessel enhancement filter is applied to segment fibers of different diameters. Morphological operations are then employed to extract the fiber centerlines, from which a 3D connectivity map is computed. Applying this approach to an initial data set yielded 2% equal error rate for segmentation and 92% accuracy for end-to-end fiber tracing (22 out of 24 hand-traced fibers). Future work calls for scaling up the algorithm to process much larger brain datasets (terabytes and above) and performing graph-based long-range connectivity analysis. This work has the potential to extend our knowledge on brain networks at the cellular level.