Flint, a type of hard rock is one of the materials used in ancient times to build a variety of sharp objects such drills and weapon heads. This skill of chiseling the stone into sharp objects is known as flintknapping. One of the early uses of materials in humans was in dentistry. Neandertals and modern humans used toothpicks made of wood or bones. Even before humans started farming 10,000-15,000 years ago, more sophisticated forms of tooth-digging methods using sharp objects made of Flint were explored.
Flint, a type of hard rock is one of the materials used in ancient times to build a variety of sharp objects such drills and weapon heads. This skill of chiseling the stone into sharp objects is known as flintknapping.
These methods involved scratching or levering of the tooth, and were neither superficial like using a toothpick to remove food nor deep-drilling to remove decaying tooth.
Tooth Worm depicted in the ivory sculptures by the Sumerians around 5000 BC .
Oral cavities bear a resemblance to holes created in wood by worms. Thus, tooth worms were thought to be the cause of tooth decay from ancient time in various cultures (Indian, Sumerian, Egyptian, Japanese, and Chinese) until the early part of the millennium (the 1300s). Of course, now we know, oral bacteria, such as Streptococcus mutans are one of the causes. These bacterias convert carbohydrates into enamel-destroying acids. Scientists think that increase in the use of a carbohydrate-rich diet, that started before the advent of farming and grew as agriculture became more common, as a cause for the rise in tooth decay.
Bow and flint-tipped drill reconstructed to mimic the once used to drill into a cavity into molar teeth. 
Beeswax-filled tooth. The figure is a micrograph. Beeswax-covered surface of a tooth crown is within the yellow dotted line.
During the Indus valley civilization (7,500-9,000 years ago), Flint-based drill heads were used in drilling deep (up to 3 millimeters wide, and 3.5 millimeters deep) into rotten dental tissues to perhaps relieve pain or treat infections. Bead artisans were thought to be suppliers of these drill bits. The scientists who conducted this study speculated that given the extent of the drilling, some filling must have been placed in the cavity.
Beeswax, embedded in a deep tooth cavity of 6,500-year-old jawbone recovered near Italy, is one of an oldest documented case of material used to fill tooth cavity. The beeswax was probably used as filler to mitigate pain and swelling.