In the growing field of virtual auditory display, personalized head-related transfer functions (HRTFs) play a vital role in establishing an accurate sound image for mixed and augmented reality applications. In this work, we propose an HRTF personalization method employing convolutional neural networks (CNN) to predict a subject HRTFs for all directions from their scanned head geometry. To ease the training of the CNN models, we propose novel pre-processing methods for both the head scans and HRTF data to achieve compact representations. For the head scan, we use truncated spherical cap harmonic (SCH) coefficients to represent the pinna area, which is important in the acoustic scattering process. For the HRTF data, we use truncated spherical harmonic (SH) coefficients to represent the HRTF magnitudes and onsets. One CNN model is trained to predict the SH coefficients of the HRTF magnitudes from the SCH coefficients of the scanned ear geometry and other anthropometric measurements of the head. The other CNN model is trained to predict SH coefficients of the HRTF onsets from only the anthropometric measurements of the ear, head, and torso. Combining the magnitude and onset predictions, our method is able to predict the complete and global HRTF data. A leave-one-out validation with the log-spectral distortion (LSD) metric is used for objective evaluation. The results show a decent LSD level at both spatial \& temporal dimensions compared to the ground-truth HRTFs and a lower LSD than the boundary element method (BEM) simulation of HRTFs that the database provides. The localization simulation results with an auditory model are also consistent with the objective evaluation metrics, showing the localization responses with our predicted HRTFs are significantly better than with the BEM-calculated ones.