Invariance against rotation of 3D objects is one of the essential properties for 3D shape analysis. Recently proposed algorithms (e.g., [9], [10], [12], [13]) have achieved rotationally invariant 3D point set analysis by using inherently rotation-invariant 3D shape features, i.e., distances and angles among 3D points, as input to Deep Neural Networks (DNNs). The DNNs capture spatial hierarchy and context among the geometric features to produce accurate analytical results. In this paper, we delve further into the DNN-based approach to rotation-invariant and highly accurate 3D point set analysis. In particular, we focus our attention on segmentation of 3D point sets, which is one of the most challenging among 3D point set analysis tasks. We propose a novel DNN for 3D point set segmentation called Rotation-invariant and Multi-scale feature Graph convolutional neural network, or RMGnet. Our RMGnet is more flexible than the previous methods as it accepts as input any handcrafted 3D shape features having rotation invariance. In addition, to accurately segment 3D point sets composed of parts having various sizes, we randomize scales at which handcrafted features are extracted and perform multi-resolution analysis of the features by using the DNN. Experimental evaluation demonstrates high segmentation accuracy as well as rotation invariance of the proposed RMGnet.