Traditional methodologies for precise inspection of bridges (pavement, beams, column cap, column, joints and inside box girder, etc.) with By-bridge equipment, Aerial Work Platform (AWP) or via ropes have several limits that can be overcome by using Unmanned Aerial Vehicles (UAVs). The constant development in this field allows us to go beyond the manual control and the use of a single UAV. In the context of inspection rules, this research provides new inputs to the multilevel approach used today and to the methods of structural inspection with drones. Today, UAV-based inspections are limited by manual and/or semi-automatic control with many restrictions on trajectory settings, especially for areas of difficult access with Global Navigation Satellite Systems (GNSS) denied that still require the intervention of a human operator. This work proposes the use of autonomous navigation with a fleet of UAVs for infrastructural inspections. Starting from a digital twin, a solution is provided to problems such as the definition of a set of reference trajectories and the design of a position controller. A workflow to integrate a generic Bridge Management System (BMS) with this type of approach is provided.