Movable antenna (MA) has attracted increasing attention in wireless communications due to its capability of wireless channel reconfiguration through local antenna movement within a confined region at the transmitter/receiver. However, to determine the optimal antenna positions, channel state information (CSI) within the entire region, termed small-scale channel map, is required, which poses a significant challenge due to the unaffordable overhead for exhaustive channel estimation at all positions. To tackle this challenge, in this paper, we propose a new convolutional neural network (CNN)-based estimation scheme to reconstruct the small-scale channel map within a three-dimensional (3D) movement region. Specifically, we first collect a set of CSI measurements corresponding to a subset of MA positions and different receiver locations offline to comprehensively capture the environmental features. Subsequently, we train a CNN using the collected data, which is then used to reconstruct the full channel map during real-time transmission only based on a finite number of channel measurements taken at several selected MA positions within the 3D movement region. Numerical results demonstrate that our proposed scheme can accurately reconstruct the small-scale channel map and outperforms other benchmark schemes.