Fabrication process of ICs
An IC is a kind of 'additive manufacturing' approach where the various features are deposited on a base material, the silicon wafer (or germanium, etc.)

Each type of added material that makes up a semiconductor - doping, diffusion, poly, metallization, contacts, oxide insulators and so forth - needs a different set of chemicals and process parameters for that material. Because of their differences, it's not possible to combine them in one step without them interfering with each other.

Using layers separates the types of materials used at each process stage so that each additive step can work its best.