Ion beam induced ripple formation in Si wafers was studied by two complementary surface sensitive techniques, namely atomic force microscopy (AFM) and depth-resolved x-ray grazing incidence diffraction (GID). The formation of ripple structure at high doses (~7x1017 ions/cm2), starting from initiation at low doses (~1x1017 ions/cm2) of ion beam is evident from AFM, while that in the buried crystalline region below a partially crystalline top layer is evident from GID study. Such ripple structure of crystalline layers in large area formed in the subsurface region of Si wafers is probed for the first time through a nondestructive technique. The GID technique reveals that these periodically modulated wave-like buried crystalline features become highly regular and strongly correlated as one increases the Ar ion beam energy from 60 keV to 100 keV. The vertical density profile obtained from the analysis of Vineyard profile shows that the density in the upper top part of ripples is decreased to about 15% of the crystalline density. The partially crystalline top layer at low dose, transforms to a completely amorphous layer for high doses and the top morphology was found to be conformal with the underlying crystalline ripple.