Cross sectional scanning tunneling microscopy (X-STM) has now become a well established method for the investigation of the structural and electronic properties of semiconductor nano-structures down to the scale of individual impurity atoms. Nevertheless, some aspects still remain challenging, for example in the sample preparation by cleavage as well as in the quantitative interpretation of the results. We present a brief overview of the techniques and geometries employed to cleave different semiconductors such as the lll-V materials, mainly GaAs, and the elementary semiconductors Si and Ge. Furthermore, we discuss the inevitable impact of the surface on the properties of the addressed impurities. This is mainly an issue when the surface reconstruction creates electronic surface states in the band gap. But also the unreconstructed GaAs(110) surface significantly modifies the symmetry of acceptor wave functions and the binding energy of donors and acceptors in the first few atomic layers. The impact of the tip will be addressed as a third quite important challenge, which is frequently neglected in the analysis of X-STM data. On surfaces with an unpinned Fermi level, the presence of the STM tip and the voltage applied to the tunneling contact significantly modifies the spectral positions of the observed electronic states and bands. Furthermore, different band bending situations open up qualitatively different tunneling paths to address individual electronic states in the sample. Detailed knowledge of the tunneling mechanism and of the tip properties, mainly apex radius and work function, is required in order to correctly extract the energetic levels from the tunneling spectroscopy data.