Ge dots grown by molecular beam epitaxy on Si(100) substrates and subsequently capped with a IO-nm thick epitaxial Si layer were investigated by means of in-situ scanning tunneling microscopy (STM), scanning tunneling spectroscopy (STS) and ballistic electron emission microscopy (BEEM). At the well-ordered and mostly flat Si surface, protrusions up to 0.35 nm in height were found at a density equal to the island density before capping. Additionally, holes caused by a directed Si diffusion away from highly strained regions could be observed. The lateral in-plane strain was determined from the elastic deformations measured by STM. Due to this inhomogeneous strain a change of the electronic surface structure occurs, resulting in a lowering of the surface band-gap on top of the buried islands. It was also possible to detect the buried islands by BEEM even though no more protrusions could be found on the surface of an additionally deposited CoSi2 film.