Neurons primarily communicate through release of neurotransmitter from presynaptic specialisations along their axonal arborisations. In order to understand the functional role of a specific neuron, it is therefore of great interest to know the structure of its axon. In particular, long-range axonal projections are thought to be important for communication between different brain regions. The mouse whisker system provides unique opportunities to investigate structure function relationships in the mammalian neocortex. The whisker primary somatosensory cortex (SSp-bfd) of mice contains a somatotopic map such that each whisker on the snout is individually represented by an anatomically-defined "barrels". Each barrel column in SSp-bfd primarily processes tactile sensory information from its homologous whisker. However, pyramidal neurons in wS1 signal information to many downstream targets, and even a single whisker deflection can evoke sensory signals across many brain areas. In this PhD thesis, I take advantage of this well studied system and aim to 1) describe important anatomical pathways involved in whisker-related learning, 2) reconstruct detailed morphology at the single neuron level in the whisker related primary sensory area (SSp-bfd), and finally 3) map neural projections in a cell-type specific and layer specific manners in the SSp-bfd and secondary sensory area (SSs). To address these aims, I adopted multiple forms of sample labeling, pre-treatment, microscopy and image processing method suitable for the specific question.