Many real-world robot applications, as found in precision agriculture, poultry farms, disaster response, and environment monitoring, require search, locate, and removal (SLR) operations by autonomous mobile robots. In such application settings, the robots initially search and explore the entire workspace to find the targets, so that the subsequent robots conveniently move directly to the targets to fulfill the task. A multi-layer robot navigation system is necessary for SLR operations. The scenario of interest is the removal of broiler mortality by autonomous robots in poultry barns in this paper. Daily manual collection of broiler mortality is time- and labor-consuming, and an autonomous robotic system can solve this issue effectively. In this paper, a multi-layer navigation system is developed to detect and remove broiler mortality with two robots. One robot is assigned to search a large-scale workspace in a coverage mode and find and locate objects, whereas the second robot directly moves to the located targets to remove the objects. Directed coverage path planning (DCPP) fused with an informative planning protocol (IPP) is proposed to efficiently search the entire workspace. IPP is proposed for coverage directions in DCPP devoted to rapidly achieving spatial coverage with the least estimation uncertainty in the decomposed grids. The detection robot consists of a developed informative-based directed coverage path planner and a You Only Look Once (YOLO) V4-based dead bird detector. It refines and optimizes the coverage path based on historical data on broiler mortality distribution in a broiler barn. The removal robot collects dead broilers driven by a new hub-based multi-target path routing (HMTR) scheme, which is applicable to row-based environments. The proposed methods show great potential to navigate in broiler barns efficiently and safely, thus being a useful component for robotics. The effectiveness and robustness of the proposed methods are validated through simulation and comparison studies.