The manipulation of the antiferromagnetic interlayer coupling in the epitaxial Fe/Cr/Fe(001) trilayer system by moderate 5 keV He ion beam irradiation has been investigated experimentally. It is shown that even for irradiation with very low fluences (10^14 ions/cm^2) a drastic change in strength of the coupling appears. For thin Cr-spacers (below 0.6 - 0.7 nm) the coupling strength decreases with fluence, becoming ferromagnetic for fluences above (2x10^14 ions/cm^2). The effect is connected with the creation of magnetic bridges in the layered system due to atomic exchange events caused by the bombardment. For thicker Cr spacers (0.8 - 1.2 nm) an enhancement of the antiferromagnetic coupling strength is found. A possible explanation of the enhancement effect is given.