Focused Electron Beam Induced Processing (FEBIP) is a technique used for etching and deposition of micro- and nano-structures using a focused electron beam. FEBIP is commonly carried out in a Scanning Electron Microscope (SEM) with a Gas Injection System (GIS) allowing precursor molecule vapors to be introduced on the substrate where they interact with the focused electron beam. Results of this work shine light on the influence of residual Water and Carbon containing species in the SEM chamber on etching and deposition processes. For etching HOPG (Highly Oriented Pyrolytic Graphite) and PMMA (Polymethyl methacrylate) using water vapor as precursor, it is shown that water participates in the principal chemical reaction for removal of these materials. However, when using Oxygen as precursor for etching these materials, Oxygen has a significantly reduced role in chemical reactions compared to residual water desorbing from surfaces in the FEBIP set-up. Degrees of involvement of Oxygen and Water in chemical reactions are demonstrated by combining experimental results and existing FEBIP Models. The Focused Electron Beam Induced Etching (FEBIE) contribution of Oxygen molecule Gas Phase Ionization prior to adsorption on the substrate surface is determined to be approximately 10% of the etching process for a micron size focused electron beam. A Precursor Gas Preparation System (PGPS) was designed and developed for in-situ fabrication of Metal Fluoride precursors from Xenon di-fluoride, XeF2. PGPS provided means of safe execution of FEBIP experiments without having to store large quantities of various dangerous and toxic materials. Using PGPS, Tungsten Hexafluoride precursor, WF6, was created in-situ and used in FEBIP experiments for deposition of Tungsten containing materials. This precursor allowed the elimination of both Oxygen and Carbon atoms in the precursor molecule in order to study the influence of residual Water (containing Oxygen) and residual Carbon containing species by measuring the amount of these atoms in deposit composition. Installation of a Liquid Nitrogen Cooled Plate over Substrate (without any direct contact with the substrate or GIS in the FEBIP set-up) proved to significantly reduce Oxygen and Fluorine content in deposits by eliminating the contribution of residual molecules from the chamber. Carbon content in deposits was also reduced when using Liquid Nitrogen Cooled Plate over Substrate (LNC-PoS). Non-FEB induced reactions (resulting in build-up of a contamination film on the substrate) are also significantly reduced or eliminated when using LNC-PoS in FEBIP experiments with WF6 precursor. In experiments with LNC-PoS, it is shown that the Carbon content in deposits mostly originates from substrate surface and arrives to FEB location via surface diffusion.