In two-dimensional samples, all atoms are at the surface and thereby exposed for probing and manipulation by physical or chemical means from both sides. Here, we show that we can access the same point on both surfaces of a few-layer graphene membrane simultaneously, using a dual-probe scanning tunneling microscopy (STM) setup. At the closest point, the two probes are separated only by the thickness of the graphene membrane. This allows us for the first time to directly measure the deformations induced by one STM probe on a free-standing membrane with an independent second probe. We reveal different regimes of stability of few-layer graphene and show how the STM probes can be used as tools to shape the membrane in a controlled manner. Our work opens new avenues for the study of mechanical and electronic properties of two-dimensional materials.