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In this paper, we present an online motion planning algorithm (3D-OGSE) for generating smooth, collision-free trajectories over multiple planning iterations for 3-D agents operating in an unknown obstacle-cluttered 3-D environment. Our approach constructs a safe-region, termed 'generalized shape', at each planning iteration, which represents the obstacle-free region based on locally-sensed environment information. A collision-free path is computed by sampling points in the generalized shape and is used to generate a smooth, time-parametrized trajectory by minimizing snap. The generated trajectories are constrained to lie within the generalized shape, which ensures the agent maneuvers in the locally obstacle-free space. As the agent reaches boundary of 'sensing shape' in a planning iteration, a re-plan is triggered by receding horizon planning mechanism that also enables initialization of the next planning iteration. Theoretical guarantee of probabilistic completeness over the entire environment and of completely collision-free trajectory generation is provided. We evaluate the proposed method in simulation on complex 3-D environments with varied obstacle-densities. We observe that each re-planing computation takes $\sim$1.4 milliseconds on a single thread of an Intel Core i5-8500 3.0 GHz CPU. In addition, our method is found to perform 4-10 times faster than several existing algorithms. In simulation over complex scenarios such as narrow passages also we observe less conservative behavior.