The helical nanofilament (HNF) and low-temperature dark conglomerate (DC) liquid-crystal (LC) phases of bent-core molecules show the same local layer structure but present different bulk morphologies. The DC phase is characterized by the formation of nanoscale toric focal conics, whereas the HNF phase is constructed of bundles of twisted layers. Although the local layer structure is similar in both phases, materials that form these phases tend to form one morphology in preference to the other. Targeted control of the nanostructures would provide pathways to potential applications and insight into how conditions drive a specific phase formation. Here, W624, a compound known to form the DC phase is confined in nanometer scale channels of porous anodized aluminum oxide (AAO) membranes. Within each nanochannel, the DC phase is suppressed forming the HNF structure instead, indicating the nanoscale spatial limitation can control the phase structure of the DC phase.