After "external cleaning," the substrate surfaces, as well as removable surfaces that have been cleaned, are subjected to a period of storage and handling, where there is some degree of recontamination. This contamination can be removed in the deposition system as part of the deposition processing by Kin situ cleanings The most common forms of in situ cleaning are heating to vaporize or out-gas contaminants and plasma-surface interactions, which desorb contaminants or remove surface layers.

A plasma is a gaseous environment that contains sufficient ions and electrons, so that it is an electrical conductor. Plasmas can be formed over a range of pressures. A low-pressure plasma, formed at gas pressures of 0.1 to 30 mTorr, is used for "plasma cleaning" and "sputter cleaning;" and plasmas at 100 to 500 mTorr are used for "plasma etching." Plasmas are usually initiated and sustained by the input of energy, by accelerating electrons in an electric field so that they ionize gas atoms/molecules by ionizing collisions. The electric fields used to accelerate the electrons are generally direct current (DC) or radio-frequency (fr), or sometimes microwave frequencies. The accelerated electrons can be confined, using magnetic or electric fields. Plasmas can also be generated using a high-current, low-voltage arc discharge, or by laser ionization.

A plasma contains neutral gas atoms/ molecules; excited atoms in unstable and metastable states; radicals (uncharged molecular fragments); positive and negative ions (charged molecular fragments and ionized atoms); and new chemical species formed in the plasma, such as O3 from O2 + O. The chemical processes that occur in the plasma can make the gas/vapor more reactive chemically, and are said to "activate" the reactive gas or vapor. For example, both atomic oxygen and ozone (O3), formed from oxygen or water vapor, are more chemically reactive than molecular oxygen (O2) or H2O vapor.

Plasmas are characterized by electron, ion, radical and neutral densities; electron and ion energies (temperatures); average particle energy (plasma temperature), electrical potential of the plasma, with respect to ground; and the potential of the plasma, with respect to surfaces in contact with it.

In the plasma, the de-excitation of unstable excited species produces a radiation spectrum, extending from the ultraviolet (UV) through the optical spectrum. Bombardment of surfaces by high-energy electrons can produce "soft" X-rays. When an atom is ionized by losing an electron, energy must be given to the electron, to cause it to be ejected from the atom. The ionization energy for the first electron to be lost is typically five to 20 eV. When a single-charged ion is "lost" by combining with an electron in the recombination process, this energy is given up, producing heat. For low-pressure plasmas, recombination takes place primarily at surfaces.

When any large surface is placed in contact with a plasma, electrons are lost to the surface faster than are ions, because of their higher mobility. This generates a negative charge on the surface, with respect to the plasma and a "sheath potential" is generated between the surface and the plasma. This sheath potential can vary from a few eV, for a plasma having low-energy electrons, to many tens of eV, for surfaces bombarded by energetic electrons. This sheath potential accelerates ions from the plasma at a rate sufficient to give an equilibrium flux of electrons and ions to the surface. The magnitude of the sheath potential is determined by plasma parameters, such as electron density, electron energy, ion density and ion energy. The figure depicts the processes that occur at a surface in contact with a plasma.

Ions which are accelerated across the plasma sheath, along with electron bombardment, radiation from the plasma and surface heating from recombination and energetic particle bombardment, remove adsorbed surface species in a process called "plasma cleaning." If the plasma gas is reactive, the surface heating and energetic ion bombardment enhances chemical reactions at the surface. If the reaction products are volatile, the surface is cleaned and the process is called "reactive plasma cleaning." Air (20% O2) and oxygen are reactive plasma gases that are commonly used to remove contaminants, such as hydrocarbons, from surfaces that can withstand the oxidizing environment. Hydrogen, or forming gas, can often be used to plasma-clean oxygen-sensitive surfaces.

Reactive plasma cleaning can also be performed, using gases that etch the surface. For example, with the use of fluorine-containing plasma gases, the oxide on silicon can be removed selectively. Under the proper plasma conditions, an "etching selectivity of 50 to 100 can be obtained for the removal of silicon oxide vs. silicon. This means that the oxide is removed at a rate that is 50 to 100 times that of silicon . With the addition of oxygen to the fluorine-containing plasma, high etch rates of the silicon can be achieved.

The surface to be cleaned can be placed in the plasma-generation region of the plasma where the ionizing electron-atom collisions are taking place, or in the "afterglow" region of the plasma. In the afterglow region, the surface is not subjected to as much bombardment by energetic species, such as high-energy ions and electrons, soft X-rays, etc., as it is in the plasma-generation region. Plasma cleaning and reactive plasma cleaning are used to remove adsorbed contaminants, such as water vapor and hydrocarbons, from surfaces like glass for optical coatings, vacuum surfaces (surface "conditioning"), and ceramics for metallization. Selective etching of the oxide from silicon is used prior to depositing metallizing films for electrical contact. When the reaction products on a surface are not volatile, a compound or residue layer will form on the surface. For example, if silicone oil is present on the surface in an oxygen plasma, it will be converted into a silica (SiO2) residue, which is non-volatile.

Massive energetic particles such as ions striking a surface transfer energy directly to the surface atoms. The most common technique for obtaining energetic particles is to accelerate positive ions from a plasma, under a negative potential on a surface. If the ions have a high enough energy, they can transfer enough energy through a "collision cascade" to cause the physical ejection of a surface atom. This ejection is known as "sputtering," and occurs from a solid surface. When used to remove contaminants from a surface, the process is called "sputter cleaning." When used as a vaporization source for film deposition, the process is called "sputter deposition." For in situ sputter cleaning, argon is the inert plasma gas that is commonly used, because of its comparatively low price. Because sputtering of the surface removes material layer-by-layer, sputtering can be used to remove material to any depth desired.

Sputter cleaning can be used to remove contaminants that do not have volatile reaction products. It is also used to remove reacted layers, such as oxides, from a surface. The accelerating potential on the surface to be sputtered can be generated by applying a DC potential (electrically conductive surfaces), applying an rf potential (electrically insulating surfaces), or by creating a high sheath potential ("self-bias") on the surface.

The energetic particle bombardment of a surface not only produces sputtering of surface atoms, but it also makes secondary electrons and high-energy reflected neutrals; introduces lattice defects in the near-surface region; can entrap bombarding species; produces "recoil implantation" of surface and lattice species; causes heating; and enhances chemical reactions at the surface. These processes can be detrimental to the bombarded surface, or to other surfaces in the system.

Sputtered species can be returned to the surface by "forward sputtering" of a rough surface and by "backscattering" in a high-pressure gaseous environment. Backscattering effectively prevents the removal of surface species by sputtering, above about 100 mTorr (argon). Backscattering and forward sputtering are important effects in sputter cleaning of a surface.

In sputter cleaning, the presence of potentially reactive gases is very important, because they will become activated in the plasma and react with the subdue to be cleaned. For example, water vapor, desorbed from the system walls by the plasma, will fragment in the plasma and the oxygen species formed will react with oxygen-active surfaces. In sputter cleaning (or sputter deposition), therefore, the plasma should be as contaminant-free as possible.