A Si-crystal layer on SiO2/Si was irradiated using 0.4 MeV Kr+, Ag+, Au+ and 5.0 MeV Ag2+, Au2+ at ion fluences of 0.5 x 10(15)-5.0 x 10(15)cm(-2). The induced structural modification in a Si crystal strongly influences ion-beam channelling phenomena through the introduced point defects, damage accumulation and induced internal strain. He+ ion channelling in the ion-implanted Si structure was studied, simultaneously with the structure and surface-morphology characterization of Si-irradiated layers, in connection with the ion-implantation parameters and prevailing energy-stopping type. The dislocated atom-depth profiles in the Si layer and the Si sub-surface layer were extracted from Rutherford backscattering spectrometry in the channelling mode (RBS-C). RBS-C shows the density of gradually displaced atoms as a function of ion fluence and ion mass for 5.0-MeV-ion implantation. The relative disorder grows more progressively for Au-ion implantation, where the thicker disordered layer was also observed in connection to the higher density collision cascade comparing to Ag+ ions. This phenomenon was discussed in the frame of the structural RBS-C and surface morphological data from AFM. The axial channelling effect of He+ ions measured in the 5.0-MeV-ion-implanted Si layer is varying during 2.0-MeV-He+ channelling in consequences of the various implantation fluences. The narrowing of axial channels observed in RBS-C was correlated to the number of produced vacancies in the Si layer after ion implantation and compared to MC simulations performed by FLUX. Nanostructured surface morphology modification has been detected mainly in 0.4-MeV-implanted Si layers using atomic force microscopy (AFM) studies, where the nuclear stopping is a prevalent phenomenon. Fourier transformation infrared spectroscopy (FTIR) has shown SOI modification mainly done by Si rearrangement and modified by possible Si-O-Si bonds creation.