Reliable identification of Human Epithelial-2 (HEp-2) cell patterns can facilitate the diagnosis of systemic autoimmune diseases. However, traditional approach requires experienced experts to manually recognize the cell patterns, which suffers from the inter-observer variability. In this paper, an automatic pattern recognition system using fully convolutional network (FCN) was proposed to simultaneously address the segmentation and classification problem of HEp-2 specimen images. The proposed system transforms the residual network (ResNet) to fully convolutional ResNet (FCRN) enabling the network to perform semantic segmentation task. A sand-clock shape residual module is proposed to effectively and economically improve the performance of FCRN. The publicly available I3A-2014 data set was used to train the FCRN model to classify HEp-2 specimen images into seven catalogs: homogeneous, speckled, nucleolar, centromere, golgi, nuclear membrane, and mitotic spindle. The proposed system achieves a mean class accuracy of 94.94% for leave-one-out tests, which outperforms the winner of ICPR 2014, i.e., 89.93%. At the same time, our model also achieves a segmentation accuracy of 89.03%, which is 19.05% higher than that of the benchmark approach, i.e., 69.98%.