The ultimate goal of high-resolution microscopy, i.e., the determination of structure and chemistry on the atomic scale, has not been achieved yet. In the case of scanning tunneling microscopy (STM), the superposition of atomic and electronic structure information was found to be a critical issue, particularly for semiconductor surfaces. Here, we show that, in the case of multicomponent systems with large unit cell size, the structural analysis is further complicated by the decay behavior of the surface wave functions, which drastically influences the distance dependence of STM images. The chemical analysis at the atomic level is generally prevented by the inaccessibility of core levels due to the low-energy scale of scanning probe microscopies. However, fingerprints for particular chemical species at the atomic level can be obtained from tunneling spectroscopy independent of the chosen substrate. Here, we will focus on a particular example of iron adsorbates on different metal substrates. Finally, the possibility of achieving chemical contrast on the nanometer scale by friction force microscopy and force spectroscopy methods will be discussed.