Feature identification is an important task in many fluid dynamics applications and diverse methods have been developed for this purpose. These methods are based on a physical understanding of the underlying behavior of the flow in the vicinity of the feature. Particularly, they require the definition of suitable criteria (i.e. point-based or neighborhood-based derived properties) and proper selection of thresholds. However, these methods rely on creative visualization of physical idiosyncrasies of specific features and flow regimes, making them non-universal and requiring significant effort to develop. Here we present a physics-based, data-driven method capable of identifying any flow feature it is trained to. We use convolutional neural networks, a machine learning approach developed for image recognition, and adapt it to the problem of identifying flow features. This provides a general method and removes the large burden placed on identifying new features. The method was tested using mean flow fields from numerical simulations, where the recirculation region and boundary layer were identified in several two-dimensional flows through a convergent-divergent channel, and the horseshoe vortex was identified in three-dimensional flow over a wing-body junction.