For best results, systems should be installed in a clean, quiet environment. 60 Hz noise is pervasive in most systems. To minimize this, careful consideration must be paid to the grounding of the system components to prevent ground loops. Also, analog and digital grounds should be kept separate as much as possible to minimize high frequency noise components. One useful method for tracking noise problems is to place the beam on the edge of a mark and monitor the electron detector output with a spectrum analyzer while disconnecting various suspect noise sources.

Acoustical noise can be a significant problem, especially in systems with field-emission electron sources. In such systems the demagnification of the field emission source, and thus the demagnification of vibrations, is much less than that of LaB₆ systems. Stray magnetic fields are also a common problem. Mechanical pumps, transformers, and fluorescent lights should be moved at least 10 ft from the column if possible. The system should be well isolated from mechanical vibrations with a pneumatic table; ideally, it should also be located on the ground floor. Finally, the temperature should be well controlled, ideally to within a tenth of a degree. This is particularly important if good placement accuracy is required.