© 2017 IEEE.In this paper, we address the estimation, control, navigation and mapping problems to achieve autonomous inspection of penstocks and tunnels using aerial vehicles with on-board sensing and computation. Penstocks and tunnels have the shape of a generalized cylinder. They are generally dark and featureless. State estimation is challenging because range sensors do not yield adequate information and cameras do not work in the dark. We show that the six degrees of freedom (DOF) pose and velocity can be estimated by fusing information from an inertial measurement unit (IMU), a lidar and a set of cameras. This letter discusses in detail the range-based estimation part while leaving the details of vision component to our earlier work. The proposed algorithm relies only on a model of the generalized cylinder and is robust to changes in shape of the tunnel. The approach is validated through real experiments showing autonomous and shared control, state estimation and environment mapping in the penstock at Center Hill Dam, TN. To our knowledge, this is the first time autonomous navigation and mapping has been achieved in a penstock without any external infrastructure such GPS or external cameras.