The cleaning and shaping of the root canal is a key procedure in root canal treatment. The aim of cleaning is the removal of tissue remnants and bacterial biofilms in order to allow close adaptation of the root filling to the canal walls. In simple straight canals with a round cross-section, this aim is easily attained by mechanical instrumentation and irrigation. The task of cleaning presents a greater challenge in oval canals, curved canals, and in canal systems that contain an isthmus. In areas that are inaccessible to mechanical instrumentation, the cleaning greatly depends on the action of sodium hypochlorite, which is used to dissolve and remove all of the remaining tissues and bacterial biofilms. Traditional irrigation with syringe and needle is often ineffective in cleaning such inaccessible areas. Newer irrigation methods allow for better cleaning by facilitating a more effective flow of irrigants; nevertheless, adequate, larger, mechanical preparations are required for the effective use of these methods. An alternative approach is to use a hollow file that adapts itself to the cross-section of the canal, without excessive enlargement of the canal, thus allowing mechanical scrubbing of the walls with a continuous flow of the irrigant through the file. All cleaning methods reach their limit in cases of long narrow isthmuses that are often inaccessible to mechanical instrumentation; adequate instrumentation is, however, a prerequisite for all cleaning methods.