This letter addresses the 3D coverage path planning (CPP) problem for terrain reconstruction of unknown obstacle rich environments. Due to sensing limitations, the proposed method, called CT-CPP, performs layered scanning of the 3D region to collect terrain data, where the traveling sequence is optimized using the concept of a coverage tree (CT). A modified TSP-based tree traversal strategy is proposed. The CT-CPP method is validated on a high-fidelity underwater simulator and the results are evaluated in comparison to an existing terrain following CPP method (TF-CPP). The CT-CPP with TSP optimizer yields significant improvements in trajectory length, energy consumption, and reconstruction error.