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Pitted rust is a common problem when dealing with body panels. The "best" way to deal with it is generously cut it out, and replace it with new metal. However, this isn't always practical, so it's frequently handled by mechanically and/or chemically removing the rust, "filling" the pitted areas with a purpose-specific product, and priming.
 What causes pitted rust?
All bare steel degrades in the presence of water (such as the water in air). Rust pitting is caused by a localized lack of oxygen in metal. This causes a small area to become anodic (it readily gives up electrons), while the slightly more oxygen-rich surrounding area becomes cathodic (readily accepts electrons), accelerating the local formation of rust. For more details, see What is rust?
Pitted rust can be more insidious than surface rust. While the pits may comprise only a small volume of a piece of metal, the widespread perforation can compromise the overall structure of the metal.
 How to fix pitted rust
Ideally, any pitted rust is cut out and replaced with new metal. Few situations are ideal, so it's common to remove the rust and fill the pits with one of various fillers, epoxies, or filler-like products.
 Removing the rust in the pits
First, all visible rust must be removed using one or more of the methods listed below.
 Mechanical removal of pitted rust
- A spot blaster is useful for this.
- Also, the following can be used: metal brush, grinding wheel, die grinder, a wire wheel on a drill. 3M Clean-n-strip discs, Lava wheels.
 Chemical removal of pitted rust
- Let naval jelly sit on the area, overnight if possible. Cover it with plastic wrap to keep it from drying out.
- If it's practical to remove and soak the panel or part, there is also the option of using electrolysis for rust removal or using one of several products that require a rusted part to be completely immersed.
- Another alternative is to use phosphoric acid. It is readily available at home centers such as Home Depot under the brand name Phosphoric Plus. It may be brushed on or a part may be soaked in the solution. Heavy pitting will take multiple applications with some wire brushing in between to speed the process. The chemical reaction of the phosphoric acid with iron oxide produces black, water-soluble iron phosphate, which can be scrubbed off. A follow up passivating treatment containing zinc phosphate, such as PPG DX520, can be used to prevent flash rusting. Phosphoric acid rust-removing products may or may not contain zinc phosphate, so read labels and directions carefully.
 DIY electrolytic rust removal for smaller parts
 Removal with heat
- Heat the pitted area until it glows, then cool it with oil on a rag. This fix should only be used on small areas because it can warp the surrounding metal, causing wrinkles and shrink marks.
 Wire feed spray welding
Newer methods introduced to the market include 'spray welding', where molten galvanized metal is sprayed on the rust pitted area until it is covered. See this video for an example.
 Welding rust pinholes
Rust pinholes can be difficult to repair because the "hole" is usually more like a "crater". The hole itself is at the bottom of a thinned-out, crater-like area of metal. First, remove any rust using the above methods. Then, these methods have been mentioned:
- Clamp a piece of copper to the other side of the panel, covering the pinhole. Weld won't stick to the panel, and will act as a heat sink so the panel doesn't warp as much. Then, fill the hole in with a MIG welder. When done, unclamp the copper.
- Drill a hole though the pinhole that is just large enough to remove the jagged edges of the rust hole. If this hole is smaller than 1/8" just fill the hole with weld material. If the hole is bigger than 1/8" and smaller than 3/8" get a nail that the shank will fit though the hole but that the head won't. Remove any coating from the nail. Put the shank though the hole from the back side. Hold the nail's shank while welding the nail to the panel. Be sure to hold the nail tight against the inside of the panel. After the weld has cooled cut off the shank of the nail and grind the substrate smooth. If the hole is bigger than 3/8" it is time to begin cutting out larger areas of metal and welding in new sheetmetal. Before you start any welding process make sure to apply weld though primer to provide proper protection from future rust.
- Solder filling can be done with specially formulated flux and solder combinations at temperatures as low as 350 degrees Fahrenheit.
 Filling in the pits
Now that the rust has been removed, the pitted area of bare metal has to be filled. First, clean with a wax and grease remover (confirm this, and add other cleaning/coating options here). Then, the pits are typically filled by priming with a high-build primer, filler or similar product. Generally, the less product used, the better. However, it may be necessary to repeatedly prime and block sand to fill the pits.
If the metal is to be chromed, then the pits should be filled with lead-free solder and then block sanded to contour.