Interaction between defects, introduced in multilayer SiGe/Si heterostructures by high energy ions, and strained SiGe layers is studied by means of high resolution X-ray diffraction, transmission and scanning electron microscopy, and electrical measurements. It has been found that implantation and subsequent annealing lead to decreased thickness of SiGe layer with increased Ge content in Ge - containing layer. Formation of precipitates in SiGe layers is strongly depended on the strain, the Ge content in SiGe layer, and the regime of ion implantation.