Over the years, the scientific interest towards 3D models analysis has become more popular. Problems such as classification, retrieval and matching are studied with the idea to offer robust solutions. This paper introduces a 3D object classification method for non-rigid shapes, based on the detection of key points, the use of spectral descriptors and deep learning techniques. We adopt an approach of converting the models into a "spectral image". By extracting interest points and calculating three types of spectral descriptors (HKS, WKS and GISIF), we generate a three-channel input to a convolutional neural network. This CNN is trained to automatically learn features such as topology of 3D models. The results are evaluated and analyzed using the Non-Rigid Classification Benchmark SHREC 2011. Our proposal shows promising results in classification tasks compared to other methods, and also it is robust under several types of transformations.