Aluminum anodizing uses fairly aggressive wet chemistry, and generally is done on complete surfaces. regions can be masked so that they do not anodize, again usually on a large area sort of scale. I think this technology would be challenging to implement at transistor like scales.
The problem that you will encounter, which will be much worse at the small scale is auto-oxidation of aluminum. no fresh surface of aluminum will remain a pure conductor for very long. The accumulation of Aluminum oxide at the surface will convert it over time from a conductor to a semi-conductor to an insulator. The rate of this change is driven by a number of external factors. As a result of this oxidation , Aluminum is also difficult to make a solder connection to.
In short there are reasons that aluminum is typically not used in integrated circuit manufacturing.