Over the last years, a rapid evolution of unmanned aerial vehicle (UAV) usage in various applications has been observed. Their use in indoor environments requires a precise perception of the surrounding area, immediate response to its changes, and, consequently, a robust position estimation. This paper provides an implementation of navigation algorithms for solving the problem of fast, reliable, and low-cost inventorying in the logistics industry. The drone localization is achieved with a particle filter algorithm that uses an array of distance sensors and an inertial measurement unit (IMU) sensor. Navigation is based on a proportional–integral–derivative (PID) position controller that ensures an obstacle-free path within the known 3D map. As for the full 3D coverage, an extraction of the targets and then their final succession towards optimal coverage is performed. Finally, a series of experiments are carried out to examine the robustness of the positioning system using different motion patterns and velocities. At the same time, various ways of traversing the environment are examined by using different configurations of the sensor that is used to perform the area coverage.