In light of recent progress in the fabrication and diagnostics of nanostructures and surfaces, more advanced spectroscopic and imaging methods are necessary in order to elucidate the detailed structure, nature and creation of such microsystems. We present here one especially promising method, namely highly charged ion surface interaction using an electron beam ion trap (EBIT) facility. Specifically we focus on the microspectroscopy, nano-and subnanostructure modification of surfaces and generation of x-rays involving heavy highly charged ion-structure interaction. In this process a large amount of potential energy is deposited by single ions at the surface leading to localized surface defects of subnanosize. In particular, we present new results on highly charged Bi q+ (q = 50-71) ions interacting with gold surfaces. A detailed experimental and theoretical analysis is provided for the x-ray spectra from the gold surface. These data have been measured at the Lawrence Livermore National Laboratory EBIT highly charged ion facility. The comparison of our computer simulation with experimental x-ray spectra provides evidence for the formation of subsurface hollow atoms. A striking orbital (n) and angular momentum (l ) dependence for hollow atoms formation has been found shedding more light on the dynamics of complex ion-surface and ion-solid interaction processes. Finally, new developments in imaging on nano-and angstrom-scale using heavy highly charged ions are discussed.