This paper studies the effects of an electron beam and an ion beam in sample preparation at the borderless bit-line contact (CB) between a transistor and a bit line in a deep trench capacitor DRAM  using the Transmission Electron Microscope (TEM) and the Electron Energy Loss Spectroscope (EELS). An abnormal region in the Si substrate was observed using cross-sectional TEM (XTEM) analysis at both the opened and un-opened CB contacts when normal sample preparation procedures were applied. CBED (Convergent Beam Electron Diffraction) in the TEM verifies this region is a structure of amorphous Si. The EELS spectrum shows the relative thickness (t/λ) of the TEM sample at this amorphous region is similar to that of the single crystal Si substrate. Experimental results demonstrated that this region was the result of radiation damage caused by either the ion-beam scan or the ion-beam Pt metal deposition required for sample preparation in the Focused Ion Beam (FIB) system. This radiation damage was not caused by inline wafer processing. However, the radiation damage zone for an un-opened contact is smaller than that for an opened contact. The size of the radiation damage zone increases relative to the time of the ion beam exposure. Using electron-beam scan and electron-beam Pt metal deposition can prevent this radiation damage from occurring.