Wafers are one thing which may be used for the substrate.
Depositing Silicon is another. The gas Silane or SiH4 is likely used to deposit silicon. The gas can be broken down in a number of ways, one is RF. Lots of other gases in the Hydride family are used in processing Silicon.
You can dope with other Hydride gases like Germane (Germanium) and Phosphine (Phosphorus) and Diborane (Boron).
Metalization can be done by electron beam evaporation or RF sputtering. The latter I have used. The e-beam system I repaired. Wires to pins can be attached with ultrasonics and typically gold wires.
In certain analog circuits, resistors can be laser trimmed through the passivation,