The Internet of Drones (IoD) ecosystem consists of many interlinked commercial services provided by a network of drones. The advent of 6 G networks plays a crucial role in increasing the feasibility of the IoD ecosystem. This ecosystem's sheer size and low computational efficiency create challenges in maintaining compliance and control. The 6 G IoD ecosystem can incorporate a blockchain-based multi layered compliance and control system to solve the significant trust and authentication issues. Implementing authentication mechanisms and UAV-user identity data in the blockchain layer can preserve the integrity of these authentication mechanisms. This paper proposes a novel Multi Layered Blockchain assisted 6 G Internet of Drones (MLB-IoD) ecosystem that augments the IoD ecosystem with secure control and compliance mechanisms. The MLB-IoD ecosystem consists of the novel Global Compliance System (GCoS) and the Swarm Security (SSe) system as its constituents. The GCoS assures drone takeoff compliance and optimally permissible route planning, while the SSe system provides intelligent swarm access control mechanisms. The analysis of the proposed MLB-IoD ecosystem reveals it to be highly secure against authentication based and cryptological attacks. Further, the simulation results show that the location-compliance based path planning module in the GCoS reduces the average flight time for UAVs by 18.37%.