Recent data indicate that unconscious masked priming can be mediated by top-down attentional set, so that priming effects of congruence between a masked prime and a subsequent probe vanish when the congruence ceases to be task relevant. Here, we show that, while the attentional set determines masked priming for color and orientation features, it does not fully determine priming based on the topological properties of stimuli. Specifically, across a series of different choice-RT tasks, we find that topological congruence between prime and probe stimuli affects RTs for the probes even when other stimulus information (e.g., color or orientation) is required for the response, whereas congruence priming effects of color or orientation occur only when these features are response relevant. Our results suggest that changes in topological properties take precedence over task-directed top-down attentional modulation in masked priming.