Three dimensional (3D) integration technology provides a great opportunity for reconfigurable device to improve performance, while the literatures for 3D reconfigurable device are lack of an efficient task scheduling and placement algorithm. In this paper, a Maximal Empty Cuboids (MECs) list is proposed to manage free space on 3D reconfigurable device. When a task is assigned or removed, a series of MECs are selected and cut into multiple Maximal Empty Rectangles (MERs) or MECs in the horizontal direction and stored in different layers. By updating the MERs in each layer and extending them from bottom to up layer, the updated MECs can be generated quickly. The experimental results verify the efficiency of proposed algorithm.