Excavation usually takes place from the top (normally this is where the latest deposits are) downwards to the earliest deposits on the site. Investigating and recording stratigraphy, finds, structures and inter-cutting features is often a highly complex and difficult process; on development led excavations this is made all the more challenging by time constraints. Archaeologists gradually build up skills and experience that help them to distinguish and interpret the mass of buried deposits which they encounter.

The quickest method of excavation is to remove soil using a machine excavator. A tracked or wheeled vehicle with an extendable hydraulic cutting bucket, such as a JCB, can be used to remove large quantities of earth in bulk. Where there is material above the archaeological layers that needs to be removed before any excavation can start, such as the concrete foundations of a demolished building, these machines are invaluable. In the hands of skilled drivers, with clear direction from a watching archaeologist, machine excavators can be used with reasonable precision to remove individual layers, and can prepare flat surfaces for further investigation. However, when they begin to penetrate archaeological deposits, it is difficult to keep track of finds discoveries and the top of fragile structures may be damaged.

When it is not appropriate to use a mechanical excavator, archaeologists must remove soil by hand. A variety of tools are used. Spades and mattocks (a flat-edged pick) can be used to remove soil quickly. Four-inch blade hand trowels are perhaps the best-known tool used by excavators, and in experienced hands can be used to separate and clean archaeological layers and features very effectively. Most archaeologists have their own personal trowel. Trowelling is used to scrape clean surfaces over areas which sometimes extend to hundreds of square metres, exposing differences in soil colouration and texture which are indicative of ancient structures, pits, ditches or deposits. On some harder surfaces, brushing is also a useful cleaning technique. For precision work, such as exposing the bones of a skeleton or gently removing soil around a fragile artefact, smaller trowels, paintbrushes, spoons and even dental tools are used.

The soil and other material that is removed is called 'spoil' and is taken away in buckets and wheelbarrows. Sometimes a proportion of the spoil is wet or dry-sieved for small artefacts which may have been missed by the excavator. This may be up to 100% of the fills of small important features but is usually a smaller percentage of large bulk deposits. Samples of soil are also taken for environmental processing, dating and geochemical analysis. These are bagged and may be processed on-site or later in a laboratory. The spoil that is left over is put on a 'spoil heap' and may be used to back-fill the excavation trenches when they