Aerial manipulators based on conventional multirotors can conduct manipulation only in small roll and pitch angles due to the underactuatedness of the multirotor base. If the multirotor base is capable of hovering at arbitrary orientation, the robot can freely locate itself at any point in $\mathsf{SE}(3)$, significantly extending its manipulation workspace and enabling a manipulation task that was originally not viable. In this work, we present a geometric robust control and whole-body motion planning framework for an omnidirectional aerial manipulator (OAM). To maximize the strength of OAM, we first propose a geometric robust controller for a floating base. Since the motion of the robotic arm and the interaction forces during manipulation affect the stability of the floating base, the base should be capable of mitigating these adverse effects while controlling its 6D pose. We then design a two-step optimization-based whole-body motion planner, jointly considering the pose of the floating base and the joint angles of the robotic arm to harness the entire configuration space. The devised two-step approach facilitates real-time applicability and enhances convergence of the optimization problem with non-convex and non-Euclidean search space. The proposed approach enables the base to be stationary at any 6D pose while autonomously carrying out sophisticated manipulation near obstacles without any collision. We demonstrate the effectiveness of the proposed framework through experiments in which an OAM performs grasping and pulling of an object in multiple scenarios, including near $90^\circ$ and even $180^\circ$ pitch angles.