The goals of the present study were 2-fold. First, we wished to investigate the neural correlates of stimulus-driven processing of stimuli strongly suppressed from awareness and in the absence of top-down influences. We accomplished this using a novel approach in which participants performed an orthogonal task atop a flash suppression noise image to prevent top-down search. Second, we wished to investigate the extent to which amygdala responses differentiate between suppressed stimuli (fearful faces and houses) based on their motivational relevance. Using continuous flash suppression (CFS) in conjunction with fMRI, we presented fearful faces, houses, and a no stimulus control to one eye while participants performed an orthogonal task that appeared atop the flashing Mondrian image presented to the opposite eye. In 29 adolescents, we show activation in subcortical regions, including the superior colliculus, amygdala, thalamus, and hippocampus for suppressed objects (fearful faces and houses) compared to a no stimulus control. Suppressed stimuli showed less activation compared to a no stimulus control in early visual cortex (EVC), indicating that object information was being suppressed from this region. Additionally, we find no activation in regions associated with conscious processing of these percepts (fusiform gyrus and/or parahippocampal cortex) as assessed by mean activations and multi-voxel patterns. A psychophysiological interaction analysis (PPI) that seeded the amygdala showed task-specific (fearful faces greater than houses) modulation of right pulvinar and left inferior parietal cortex. Taken together, our results support a role for the amygdala in stimulus-driven attentional guidance toward objects of relevance and a potential mechanism for successful suppression of rivalrous stimuli.