Periodical inspection and maintenance of critical infrastructure such as dams, penstocks, and locks are of significant importance to prevent catastrophic failures. Conventional manual inspection methods require inspectors to climb along a penstock to spot corrosion, rust and crack formation which is unsafe, labor-intensive, and requires intensive training. This work presents an alternative approach using a Micro Aerial Vehicle (MAV) that autonomously flies to collect imagery which is then fed into a pretrained deep-learning model to identify corrosion. Our simplified U-Net trained with less than 40 image samples can do inference at 12 fps on a single GPU. We analyze different loss functions to solve the class imbalance problem, followed by a discussion on choosing proper metrics and weights for object classes. Results obtained with the dataset collected from Center Hill Dam, TN show that focal loss function, combined with a proper set of class weights yield better segmentation results than the base loss, Softmax cross entropy. Our method can be used in combination with planning algorithm to offer a complete, safe and cost-efficient solution to autonomous infrastructure inspection.