This chapter provides an overview of the computational multiscale modeling approach basedon utilization of the powerful and universal software packages MBN Explorer and MBN Studio. Three illustrative case studies of multiscale modeling are presented in relation to (i) development of novel sources of monochromatic high-energy radiation based on the crystalline undulators, (ii) controlled fabrication of nanostructures using the focused electron-beam induced deposition, and (iii) ion-beam cancer therapy. These examples illustrate the key algorithms and unique methodologies implemented in the software in different research areas arising in connection with the development of novel and emerging technologies.