Vegetation, trees in particular, sequester carbon by absorbing carbon dioxide from the atmosphere. However, the lack of efficient quantification methods of carbon stored in trees renders it difficult to track the process. We present an approach to estimate the carbon storage in trees based on fusing multi-spectral aerial imagery and LiDAR data to identify tree coverage, geometric shape, and tree species—key attributes to carbon storage quantification. We demonstrate that tree species information and their three-dimensional geometric shapes can be estimated from aerial imagery in order to determine the tree’s biomass. Specifically, we estimate a total of 52; 000 tons of carbon sequestered in trees for New York City’s borough Manhattan.