Multi-channel speech separation using speaker's directional information has demonstrated significant gains over blind speech separation. However, it has two limitations. First, substantial performance degradation is observed when the coming directions of two sounds are close. Second, the result highly relies on the precise estimation of the speaker's direction. To overcome these issues, this paper proposes 3D features and an associated 3D neural beamformer for multi-channel speech separation. Previous works in this area are extended in two important directions. First, the traditional 1D directional beam patterns are generalized to 3D. This enables the model to extract speech from any target region in the 3D space. Thus, speakers with similar directions but different elevations or distances become separable. Second, to handle the speaker location uncertainty, previously proposed spatial feature is extended to a new 3D region feature. The proposed 3D region feature and 3D neural beamformer are evaluated under an in-car scenario. Experimental results demonstrated that the combination of 3D feature and 3D beamformer can achieve comparable performance to the separation model with ground truth speaker location as input.