What happened to all the Aliens (Xenomorphs) that attacked the Engineers?

I agree that evidence suggests the engineers were killed by some form of the "alien" from the end of the movie.

The killing of the engineers took place long before the characters of Prometheus discover the remains of the engineers. I think the movie mentions that 2000 years appear to have elapsed.

Given that several centuries have passed -- and that, for all that time, there would have been nothing in the area for the "alien" or "aliens" to eat -- I think it is safe to assume that the alien/aliens is/are no longer alive, or at least no longer in the same part of the planet as the action in Prometheus. Either it/they starved to death, or wandered off in search of other food, or both.

What happened to the Engineers is not explained clearly in the movie, but one might make speculations from what is actually shown (I like the "black goo" expression for the substance :-) :

• the hologram of the Engineer running in the corridor, the body of the one severed by the hatch
• the result of trying to revive an Engineer('s detached head) : a biological "explosion"
• the result of a Human parasited by the "black goo snake" : a murderous "undead" monster
• the result of a Human "poisoned" by the black goo itself : some form of monster mutation also
• the result of a Human woman indirectly contaminated by the black goo through intercourse : a monster progeny

One may thus suppose that the Engineers created the black goo as a biological weapon, aiming to destroy the Human race that they initially created. However their experiments somehow backfired and they were contaminated and destroyed (except the one who went into stasis/cryo-sleep/whatever) or maybe some also managed to escape.

The "black goo snake" could be a mutation of some life form indigenous or that they brought with them, a result of experimenting on some form of "lab rats", or a result of initial Engineer contamination.

And "the" Alien (xenomorph) as seen in "later" (filmed earlier) Alien movies is only "born" from the Engineer('s consumed innards, like in Alien movies) that was attacked and parasited by the monster "born" from a Human woman('s womb), herself contaminated through intercourse, etc...

Just to add:

There is a cross-over event 'Aliens' comic titled, Fire and Stone. One story in it takes place during Aliens and a main character finds one Engineer in stasis on LV-223 from a crashed ship. So even though all of the ones in the chamber are considered dead according to the answer above me, if the comic is canon, then we know there can be more on the planet in stasis...

Set concurrently around the same time as Aliens, the narrative begins prior to the arrival of the colonial marines as seen in the film, during the Xenomorph infestation of the Hadley's Hope colony on LV-426...

As Cale and Dione continue to bicker over the group's course of action, and the xenomorphs continue to whittle down the group's numbers, Russell becomes increasingly distant from the group affairs. Having stumbled upon a probe from the Prometheus expedition decades ago, Russell analyzes the data from the probe and finds that the current landscape of LV-223 has changed drastically from what it was at the time of the previous expedition. Russell deduces that the enigmatic black substance that the members of the Prometheus expedition encountered acted as a catalyst that expedited the evolution of the environment on the planet from a barren, rocky wasteland to a lush jungle setting. Russell also explores a crashed ship of the "Engineer" species encountered in the film, and finds a dormant Engineer in stasis, although much to his dismay, he is unable to wake it. Russell continues to compile his findings and stores notes and work in a cave situated within a mountain that the xenomorphs are wary of approaching. Although he reports his discoveries to the group, Russell's findings are dismissed as unimportant in comparison to the immediate goal of survival. https://en.wikipedia.org/wiki/Fire_and_Stone