Terraforming is a process of making a barren planet into one like Terra (latin name for Earth). But how do we call the process if it is the aliens transforming the planet to their environment (let's assume such planet would be completely unhabitable for humans so unlike Terra)?

Something like "xenoforming"?

From wikipedia:

The term "terraforming" is sometimes used more generally as a synonym for planetary engineering, although some consider this more general usage an error.

So I'd either just use "terraforming" (disregarding the etymology and just using it to mean reshaping a planet), or if you wanted to be pedantic, use "planetary engineering"
Or alternatively, also from wikipedia:

H. G. Wells alludes to what today might be called "xeno-terraforming" - alien life altering Earth for their own benefit - in his 1898 novel The War of the Worlds.

+1 for Hodgman: just adapt the term of terra-forming. Many words we use today are derivation of words used in medieval times. Today the link of these words to its origin is often lost , but in the language context/vocabulary of the modern society it is still valid.

Terraforming could be such a term, which has just been adapted by the future culture to describe the transformation of a planet to be inhabited by humans or aliens.

Hmm I upvoted Erik, because a species-wide usage of "terraforming" would implicit sort of a cultural take-over.. why would aliens borrow a human word?

Each species has its own history and heritage words.. this isn't (necessarily) given up when they meet a different species.

Just another point to consider, why should there be a simple answer to a simple question after all? :)