In this paper, we consider the user positioning problem in the massive multiple-input multiple-output (MIMO) orthogonal frequency-division multiplexing (OFDM) system with a uniform planner antenna (UPA) array. Taking advantage of the UPA array geometry and wide bandwidth, we advocate the use of the angle-delay channel power matrix (ADCPM) as a new type of fingerprint to replace the traditional ones. The ADCPM embeds the stable and stationary multipath characteristics, e.g. delay, power, and angle in the vertical and horizontal directions, which are beneficial to positioning. Taking ADCPM fingerprints as the inputs, we propose a novel three-dimensional (3D) convolution neural network (CNN) enabled learning method to localize users' 3D positions. In particular, such a 3D CNN model consists of a convolution refinement module to refine the elementary feature maps from the ADCPM fingerprints, three extended Inception modules to extract the advanced feature maps, and a regression module to estimate the 3D positions. By intensive simulations, the proposed 3D CNN-enabled positioning method is demonstrated to achieve higher positioning accuracy than the traditional searching-based ones, with reduced computational complexity and storage overhead, and the ADCPM fingerprints are more robust to noise contamination.