Liquid-ordered (L(O)) domains reconstituted in model membranes have provided a useful platform for in vitro studies of the lipid-raft model, in which signalling membrane molecules are thought to be compartmentalized in sphingolipid- and cholesterol-rich domains. These in vitro studies, however, have relied on an uncontrolled phase-separation process that gives a random distribution of L(O) domains. Obviously, a precise control of the size and spatial distribution of the L(O) domains would enable a more systematic large-scale in vitro study of the lipid-raft model. The prerequisite for such capability would be the generation of a well-defined energy landscape for reconstituting the L(O) domain without disrupting the two-dimensional (2D) fluidity of the model membrane. Here we report controlling the reconstitution of the L(O) domains in a spatially selective manner by predefining a landscape of energy barriers using topographic surface modifications. We show that the selective reconstitution spontaneously arises from the 2D brownian motion of nanoscale L(O) domains and signalling molecules captured in these nanodomains, which in turn produce a prescribed, concentrated downstream biochemical process. Our approach opens up the possibility of engineering model biological membranes by taking advantage of the intrinsic 2D fluidity. Moreover, our results indicate that the topographic configuration of cellular membranes could be an important machinery for controlling the lipid raft in vivo.