We report on the onset of anti-resonant behaviour of mass transport systems driven by time-dependent forces. Anti-resonances arise from the coupling of a sufficiently high number of space-time modes of the force. The presence of forces having a wide space-time spectrum, a necessary condition for the formation of an anti-resonance, is typical of confined systems with uneven and deformable walls that induce entropic forces dependent on space and time. We have analyzed, in particular, the case of polymer chains confined in a flexible channel and shown how they can be sorted and trapped. The presence of resonance-antiresonance pairs found can be exploited to design protocols able to engineer optimal transport processes and to manipulate the dynamics of nano-objects