Ultra-high vacuum (UHV) investigations have demonstrated a successful development of atomic nanostructures. The scanning tunneling microscope (STM) provides surface study at the atomic scale. However, the surface preparation is a crucial experimental step and requires a complex protocol conducted in situ in a UHV chamber. Surface contamination, atomic roughness, and defect density must be controlled in order to ensure the reliability of advanced UHV experiments. Consequently, a packaging for nanoscale devices has been developed in a microelectronic clean room environment enabling the particle density and contaminant concentration control. This nanopackaging solution is proposed in order to obtain a Si(001)-(2 1):H reconstructed surface. This surface is protected by a temporary silicon cap. The nanopackaging process consists in a direct bonding of two passivated silicon surfaces and is followed by a wafer dicing step into 1-cm2 dies. Samples can be stored, shipped, and in situ opened without any additional treatment. A specific procedure has been developed in order to open the nanopackaged samples in a UHV debonder, mounted in the load-lock chamber of a low-temperature STM system (LT-STM). Statistical large scan LT-UHV-SEM images and LT-UHV-STM images have been obtained enabling the surface study at the atomic resolution.