Vlinder Guyot rises to a mean depth of and its flat top has dimensions of with a trapezoid shape and sometimes a cover consisting of volcanic rocks and pelagic ooze. A posterosional cone lies on the summit platform of Vlinder Guyot and rises about above it. The northern rim of the summit platform is cut by a notch that appear to have formed through a mass failure; similar mass failures have been observed on Kilauea and Piton de la Fournaise in Hawaii and Reunion respectively and in the case of Vlinder Guyot has involved over of rocks, which are now deposited over away from the collapse scar. The pedestal of the seamount lies at a depth of and covers an area of . The existence of Miocene volcanic cones reaching a depth of has been reported, which makes Vlinder Guyot the shallowest among the Magellan Seamounts; the volcanic cones form an irregular group of cones in the northeastern corner of the summit platform and they feature reefal deposits. The slopes of Vlinder Guyot feature benches and terraces as well as rectilinear grabens.