We report new and exciting experimental results on ion-induced nanopatterning of a-Si and a-Ge surfaces. The crystalline Si (100) and Ge (100) wafers were amorphized and an a/c interface was developed by pre-irradiation with a 50 keV Ar+ beam at normal incidence with an ion fluence of 5.0 × 1015 ions cm−2. These amorphized surfaces were post-irradiated with Ar+ and Kr+ beams at an angle of 60°. The post irradiation was done with ion fluences of 1.0 × 1017 ions cm−2. For each beam, two energies (50 and 200 keV for Ar+, 100 and 250 keV for Kr+) were chosen to ensure ion stopping in both sides of the a/c interface. Regular nanopatterning (in the form of ripples) is observed on the Ge surface only with the post irradiation of the Kr+ beam. The Si surface showed regular nanopatterning with the irradiation of both beams with two energies. For the ion beams crossing the a/c interface, ripples of higher amplitude and longer wavelength were formed. Further, the irradiation with a heavy beam yielded surface ripples of relatively larger amplitudes. The Raman measurements confirm amorphization of the pre-irradiated surfaces. Surprisingly, the post-irradiated Si surface with the 100 keV Kr+ beam showed evidence of recrystallization. In the paper we discuss the physics at the interface and explain the experimental findings.