A general chamber preparation procedure was developed to minimize the number of possible vacuum contaminants during thin film fabrication. While every substrate introduced to the chamber must be free of contaminants, these chamber preparations are typically only necessary after the vacuum system has been exposed to atmosphere. Thus, the following procedures are followed once before the introduction of several substrates and subsequent deposition processes. The chamber and related components discussed here are presented at length in Appendix B.4.

Before a wafer is introduced to the chamber, the chamber is baked by heating chamber walls with resistive heating straps wrapped about the exterior of the chamber. The entire chamber is typically heated to $150-200^\circ \textrm{C}$ to fully drive off any water molecules from the inner chamber walls. The contaminants degassed from walls are first efficiently pumped out by a turbomolecular pump, then finally by a cryopump that returns the chamber to its base pressure (typically $\sim 10^{-9}  \textrm{Torr}$).

During system baking, all the components of the deposition chamber are also baked. The aluminum effusion cell source is heated $\sim25-50^\circ\textrm{C}$ above anticipated deposition temperatures ($1100-1175^\circ \textrm{C}$). This allows the effusion cell to be degassed in a temperature range that the cell will not acquire during deposition, and therefore, minimize the number of contaminants degassed during Al deposition.

The electron evaporation gun used for Si diffusor depositions, is also heated to a temperature higher than normal operating temperatures. The emission current is held at 0.2 A for half an hour. This allows the evaporation source to be operated at 0.1 A (lower temperature) during Si deposition, providing minimal contamination.

The substrate heater is increased to $1000^\circ \textrm{C}$ to degas any contaminants that would otherwise contaminate the substrate during its final cleaning stage (at $700 - 900^\circ\textrm{C}$). As well, the RHEED gun is operated for several minutes, the mass spectrometer is degassed for half an hour, and the ion gauges (used to measure high to ultra-high vacuum pressure) are degassed for half an hour. All components potentially used during a fabrication sequence are degassed before introducing the substrate.