The cleaning procedures outlined in this section will be divided into three broad categories: acid solution cleaning, alkaline solution cleaning, and dry cleaning.   The first two categories involve liquid cleaning, whereby particle removal may be achieved at the same time as surface activation.   The third category will have little or no impact on particle removal, but will generally provide a rapid and simple way of activating surfaces.   The alkaline cleaning generally involves a light etching of the glass surface.   The acid cleaning, although it may leach components from the glass surface, generally does not involve an etching of the glass.

                The advantages and disadvantages of these cleaning procedures may be summarized as follows.   The liquid cleaning procedures are simple to set up and rapid to use.   However, they generate considerable waste products and require either the use of significant operator time, or the use of sophisticated machines.   As such, they are well suited to the cleaning of occasional samples in research laboratories.   
A strong caveat for these techniques is the requirement of rinsing and drying the samples.   The latter step is delicate and invariable compromises the obtaining of a uniform, clean and dry surface on the substrate.   
Vapor-degreasing (Pul84), is not discussed.   This technique relies on the condensation of vapor from a freshly-distilled solvent.   It may remove dust and organic contaminants.   It will not generally provide a glass surface that is uniformly wettable to water, due to residual organic molecules that remain adsorbed to the glass surface.   
The dry cleaning procedures require the investment in suitable equipment.   They have the advantage of being able to clean large quantities of samples with little or no waste products and little operator input.   
They also have the distinct advantage of directly generating a clean, uniformly wettable and dry surface on the substrate. 

                This is one of the most commonly used procedures for cleaning glass and silica surfaces in small research laboratories.   It has the advantage of being easy to set up, requiring the purchase of basic chemicals and the use of a fume hood.   However, it generates significant toxic waste products and is thus rarely scaled up for industrial applications.   The basic concept is that of mixing a concentrated acid with a strong oxidizing agent.

                The original formulation was the use of a saturated potassium dichromate solution in concentrated sulfuric acid. The solution, known as chromerge, was prepared by completely dissolving 20 grams of potassium dichromate (K₂Cr₂O₇) in 90 grams of water. To this was slowly added 900 grams of concentrated sulfuric acid.  The mixing reaction is highly exothermic, exposing the operator to a high risk from spattering.   This solution could be re-used as long as it remained brown, rather than green, indicating the oxidation state of the dichromate.  
The sample was dipped in the chromerge for 20 minutes, followed by 20 minutes in a 1:1 concentrated hydrochloric acid/water solution to remove chromium ions from the surface.   A pure water rinse and the drying of the sample surface follow this.   The latter should be practiced as described in the particle removal section above, taking care not to allow water streaks across the surface.   
The use of chromerge has been all but completely banned in most research and industrial establishments. This is because the chromium ion is highly toxic to the environment and poses a severe waste disposal problem, even in small quantities. Further, the hexavalent chromium present in the above solutions is considered by regulatory agencies to be a potent human carcinogen. The addition of chloride or halogens to chromerge solutions can generate the highly toxic and volatile carcinogen, chromyl chloride. This mandates the use of chromerge under a chemical fume hood.

                Chromerge cleaning, as described in the paragraph above, was found to be adequate for generating a uniformly wettable surface on the native oxide layer of a silicon crystal. This cleaned substrate, while still wet, showed uniform deposition of a charge-adsorbed monolayer of surfactant (Bir94). To obtain a uniform dry surface, this monolayer was burned off with UV/ozone radiation.   This gave excellent results for the deposition of a monolayer of anionic surfactant from a thinning film of surfactant solution (Bir95). Further, the re-hydration of this surfactant layer showed a relatively uniform thickness, indicating uniform surface properties of the hydrated substrate surface.

                As a replacement to the highly successful but toxic chromerge solution, Godax laboratories (Takoma Park, MD, USA) has developed a product called Nochromix . This is reportedly dispensed in a powder form, costing approximately $2.50 per bag.   It is added to concentrated sulfuric acid. As the solution turns brown, the solution is spent and a new package may be added to the sulfuric acid.   Due to the hygrosopic nature of sulfuric acid, it is important to keep concentrated sulfuric acid solutions closed to air while not in use. This avoids their dilution with water following prolonged exposure to air.

                Prior to the commercial existence of Nochromix , an efficient alternative to chromerge was developed. This consisted of mixing two parts concentrated sulfuric acid with one part hydrogen peroxide solution, providing the strong oxidizing agent. The mixing process is strongly exothermic, resulting in an extremely hot final solution. Cleaning with this mixture is recommended at 90° C for 20 minutes. This is followed by a rinse in pure water and careful drying as described above. This solution removes hydrocarbons from the surface of the substrate with vigor. Care should be taken when using the hot cleaning solution. It should be used under a fume hood, together with a protection against spills from the breaking of glass containers.

                Verification of a successful cleaning procedure following acid cleaning is essential. The sample should be completely wettable to water during the pure water rinse. Wettability of a surface to water in this context implies that a film of water on the surface does not dewet. Dewetting is observed when dry patches are formed where the liquid film has receded from an area of surface and they are characterized by the presence of a liquid film with thickness of order one millimeter adjacent to a "dry" zone (by visual observation). This may be further verified, if necessary, by halting the water flow and holding the substrate vertically. The water film will then thin. As it thins, light interference fringes should be observed. If dry patches are formed before the interference fringes are seen, the glass is not completely wetting in these areas and the cleaning has failed. On completion this test, the glass should immediately be re-wet with water and dried carefully as described above.

                Finally, these acid cleaning procedures are not effective for the complete removal of fluorocarbon molecules, such as perfluoro-silanes grafted to a glass surfaces. Further, poly-dimethyl siloxane (PDMS, or silicone oil) contaminants are not well removed using these acid cleaning solutions. PDMS contamination is frequently found in environments where vacuum pump oils or silicon rubber seals are used. 
The PDMS molecules adsorb strongly to glass surfaces and are generally not removed by surfactant solution cleaning or by acid cleaning. Care should be taken that no PDMS or fluorocarbon silane molecules come into contact with the acid cleaning solutions, as they may contaminate the solutions to a point where they will no longer render glass hydrophilic and may increase its hydrophobicity.

IV.2 Alkaline solution cleaning

                These solutions, generally made from sodium hydroxide (or potassium hydroxide) dissolved in water, are designed to lightly etch the glass surface. Solutions above pH 9 begin to etch glass surfaces. The manufacture of an aqueous NaOH solution is a relatively simple procedure. Its etching of the glass ensures the removal of surface residues, resulting in a clean surface. Glass may cleaned by exposing it to a saturated aqueous sodium hydroxide solution at room temperature for fifteen minutes. Should the glass be coated with a non-wetting layer, this exposure may need to be longer for the solution to attack the glass under the non-wetting layer. Alcoholic solutions of NaOH or KOH may be used to improve the wetting properties of the solution. 

The cleaning with alkaline solution should be followed by a five minute dip in 1M hydrochloric acid to neutralize the alkali attack on the glass surface. This should be followed by a   twenty minute dip in pure water. The sample should then be checked for surface cleanliness by wettability, as described in the above section, followed by a careful drying in air, as described in the particulate removal section.

                An efficient alternative to concentrated sodium hydroxide solution is the use of a surfactant known as Hellmanex.   Developed by Hellma (Müllheim, Germany), this surfactant was designed to clean quartz spectroscopy cells, without altering their optical properties and leaving no residue. Its recommended use is a one hour dip at room temperature or a 30 minute dip at 30° C for a 2% solution by weight in water. In practice, ten to twenty minutes under ultrasonic agitation have given satisfactory results. Hellmanex surfactant yields an alkaline solution of small molecule surfactant. The alkaline solution contributes to a light etching of the glass surface, while the surfactant ensures wetting of the substrate, even if coated with hydrophobic contaminants. The use a small molecule surfactant is believed to contribute to the absence of any surface residue after rinsing. Following cleaning, it may be useful to soak the substrate in pure water for twenty minutes to leach out any small molecules absorbed into the glass surface. This is followed by a pure water rinse and a careful drying, as described in the particle removal section, above. We have found this cleaning solution to exhibit excellent cleaning properties, coupled with a simple application process. Another similar alkaline small surfactant molecule cleaning powder is sold under the trade names of Alconox.

                Finally, glass surface may be etched by exposure to a solution of fluoride ions, such as that generated by an aqueous solution of hydrofluoric acid. These solutions have been included in this section, despite their being acidic, because they rely on etching the glass surface to achieve cleaning. The fluoride ions rupture siloxane bonds. These cleaning solutions are generally dilute hydrofluoric acid, of the order of a few percent in HF concentration. The concentration and cleaning time should be adjusted to the glass composition in order to achieve cleaning without excessive etching. The solutions are generally used at room temperature. More concentrated HF solutions are used to dissolve macroscopic pieces of glass. These concentrated HF solutions should not be used to clean glass surfaces, since their rapid etching increases the surface roughness of the glass. Great care should be exercised when handling hydrofluoric acid, even in dilute solutions. It is extremely toxic and skin exposure (or inhalation) can be fatal. The acid penetrates the skin and migrates in towards the bones. During its passage, it neutralizes nerve endings, causing no pain or feeling. On reaching the bone, a decalcification takes place. This may lead to a necrosis and a possible amputation.   Exposure of skin over an area approximately larger than the palm of a hand may result in heart failure. Thus, the use of hydrofluoric acid is not recommended outside of well-controlled environments.   

IV.3 Dry cleaning

                This category encompasses a several processes that clean a glass surface without touching it or significantly altering its surface composition. The machines used and their safety protection require a significantly larger capital investment than the above chemical cleaning procedures for cleaning small numbers of glass samples. They rely on high temperatures or the use of plasma to degrade and desorb contaminant hydrocarbons from the glass surface. 

The dry cleaning procedures present the significant advantage of being non-contact cleaning and resulting directly in a clean and dry substrate surface, ready to receive a subsequent coating. They generate few waste products and require minimal operator input, making them highly attractive to the scaling up required by industrial processes. Their efficiency at cleaning different types of contaminants from a variety of substrates makes them attractive for use in research laboratories.

                One of the most basic processes for cleaning glass surfaces is the use of pyrolysis. This involves heating the glass to a temperature above 300° C, generally 500 ° C for over 30 minutes. A typical cycle will consist of a rise in temperature from room temperature to 500° C over four hours, followed by five hours at 500° C and a return to room temperature over five hours. The slow increases and decreases in temperature are designed to avoid glass breakage from thermal shock. This process generates few waste products. It relies on the degradation and desorbtion of organic contaminants from the surface of the glass. It has been found to be effective in increasing the wettability of glass surfaces contaminated with any organic pollution, including such molecules as PDMS or fluorocarbons. This process may generate soot residue and is not effective in removing this soot. When using this process, it is important that the residual contamination on the glass surface be of the order of nanometer thickness or less. This is in order to avoid macroscopic residues on the glass surface, such as carbon or other inorganic matter. This technique does not remove dust particles from the glass surface. Care should be used when pyrolyzing sodalime glass, where the presence of moisture may leach alkalis from the glass, generating a sodium hydroxide residue on the glass surface. This is generally not a problem when using air with ambient humidity, provided that air circulation around the samples is limited.

                A more efficient process is the use of plasma to clean substrates. This process is suitable for industrialization and has been used in some large industrial processes. The cleaning may involve an oxygen plasma to directly oxidize hydrocarbons, or an argon plasma to degrade them and desorb them. Such processes are suitable for cleaning glass surfaces and for activating polymer surfaces. The use of a plasma bears the distinct advantage of being able to penetrate inside complex structures. Generating plasma requires a specifically designed reactor. Generally, the specific gas to be used is injected to form an atmosphere at reduced pressure. Electromagnetic radiation (RF or microwave frequency) is then coupled into the enclosure, generating the plasma.   
Some plasma systems operate at atmospheric pressure, removing the need for a vacuum-sealed enclosure. Plasma cleaning has an interesting feature, whereby its, since its "effective" temperature (its k_bT equivalent thermal energy) is of several thousand degrees. This is achieved by coupling energy into the gaseous phase without strongly increasing the substrate temperature. As an example, this process may clean carbon residue from surfaces without excessive heating. 
The plasma cleaning techniques also find application in the activation of other inorganic substrate surfaces and organic polymer surfaces.