A catheter used for treatment of complex vasculature, such as a bifurcated aneurysm, is provided with an inflatable balloon at a distal portion thereof. The shape, location and material of the inflatable balloon are selected such that when inflated, the balloon conforms to the shape of the complex vasculature, or at least a portion thereof, without appreciably deforming the vessel walls. In this manner, the balloon can be used to control flow in the vasculature, for example occluding a selected branch of the vasculature during introduction of material in order concentrate the material and minimize its disbursement by blood flow.