Instance segmentation and object detection are significant problems in the fields of computer vision and robotics. We address those problems by proposing a novel object segmentation and detection system. First, we detect 2D objects based on RGB, depth only, or RGB-D images. A 3D convolutional-based system, named Frustum VoxNet, is proposed. This system generates frustums from 2D detection results, proposes 3D candidate voxelized images for each frustum, and uses a 3D convolutional neural network (CNN) based on these candidates voxelized images to perform the 3D instance segmentation and object detection. Results on the SUN RGB-D dataset show that our RGB-D-based system’s 3D inference is much faster than state-of-the-art methods, without a significant loss of accuracy. At the same time, we can provide segmentation and detection results using depth only images, with accuracy comparable to RGB-D-based systems. This is important since our methods can also work well in low lighting conditions, or with sensors that do not acquire RGB images. Finally, the use of segmentation as part of our pipeline increases detection accuracy, while providing at the same time 3D instance segmentation.