Living cells need to deliver specific cargoes at specific locations. In order to do that, they mostly use molecular motors walking on “cytoskeletal highways”, an highly organized network of polar filaments (microtubules). Since different motors walk in different direction along the filament polarity and since the microtubule network is organized in a radial way, this allow selective transport towards the center or the periphery of the cell. How however such a network is formed in the first place remains unknown. Here we show how a minimal system comprising microtubules and of two different kinds of molecular motors, a plus- and a minus-end directed one, can self-organize in polarity-sorted domains. The motors are bound to a membrane and are hence able to both walk on them and to exert forces, hence displacing them. This creates a feedback loop in which the motors accumulate inhomogeneously in space due to directed transport and this inhomogeneity in turn leads to net forces being exerted locally on the filaments, pushing them away and creating further inhomogeneity. The final result is that starting from a homogeneous initial distribution of motors and filaments, the system self-organizes into domains enriched of motors separated by an interface of polarity-sorted microtubules. Building on this using an analogy with the classical example of Maxwell’s demon (or of microtubules as “active surfactants”) we build a continuous model showing how phase separation can be achieved by activity in the form of selective transport of material and how this process can be harvested to create ordered structures over length- and timescales much bigger than the typical ones of the microscopic constituents.