I am not an expert in this area, and this is rather an open question, but I will tell you what I know.
I assume that you are talking about a requirement to kill 'bugs' or bacteria. There are two main methods that I know of to sterilise chemical plants - temperature and chemical. Temperature sterilisation is normally carried out with steam. The main issue with using steam, is that you need to make sure that the materials in contact with it are able to withstand the temperatures involved, and that the water is acceptable in the product/other material. You need to maintain the temperature in excess of 100°C for at least 15 minutes to ensure a reasonable degree of sterilisation (The higher the temperature or the longer the time, the better, as rate of kill is an exponential decay). Temperatures below 100°C can be used for a longer period of time. 70°C is acceptable if held at a minimum of 70°C for at least 4 hours. This is technically pasteurisation rather than sterilisation, but it will work for the majority of bugs, especially in areas where the temperature is more easily controlled, such as batch reactors - don't go below 70°C though, as it doesn't work below this, and at 25 - 40°C, they reach their ideal incubation temperature and so will rapidly multiply.
Chemical sterilisation involves the use of chemicals that are toxic to the bugs - commonly used materials are sodium hypochlorite (Bleach), chlorine dioxide, sodium bisulphite, and there are a whole host of proprietary bactericides. Choice really depends on chemical compatibility with your product and with materials of construction. The time required for sterilisation varies between the chemical used, but is generally in the order of hours.
All of the above are dependent on plant design. Dead spots should be eliminated. Basically, this means design and build to cGMP (Good Manufacturing Practice). An existing plant is unlikely ever to be perfect in this respect, unless it is built to cGMP in the first place, but some things can be done to improve the design, e.g. by removing blanked off stubs, replacing valves with hygienic valves etc. There are many consultants who can advise you on this.
